CINXE.COM
Bioconductor Tutorials
<html> <head> <title> Bioconductor Tutorials </title> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="icon" href="/static/favicon.ico" type="image/x-icon"/> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <!-- Global site tag (gtag.js) - Google Analytics --> <script async src="https://www.googletagmanager.com/gtag/js?id=UA-55275703-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag() { dataLayer.push(arguments); } gtag('js', new Date()); gtag('config', "UA-55275703-1"); </script> <link rel="stylesheet" href="/static/CACHE/css/output.b3e21268cb4d.css" type="text/css"> <script src="/static/CACHE/js/output.10280c94381d.js"></script> </head> <body itemscope itemtype="https://schema.org/QAPage"> <div class="ui inverted container main"> <span class="menus"> <div class="ui top attached text menu" id="menu-topics"> <div class="ui inverted dimmer"></div> <div class="right menu" id="login-opts"> <a class="item " href="/accounts/login/"> <i class="sign-in icon"></i>Log In</a> <a class="item " href="/accounts/signup/"> <i class="user icon"></i> Sign Up</a> <a class="item " href="/info/about/"> <i class="info icon"></i>about</a> <a class="item " href="/info/faq/"> <i class="question icon"></i> faq </a> </div> </div> <div class="ui labeled icon attached pointing menu" id="menu-header"> <div class="header item" id="logo"> <a href="https://support.bioconductor.org/"><img class="ui image" src="/static/transparent-logo.png"></a> </div> <a class="item format add-question" href="/new/post/"> <span class="">Ask a question</span> </a> <a class="item format " href="/"> <span class="">Latest</span> </a> <a class=" item format" href="/t/news/"> <span class="">News</span> </a> <a class=" item format " href="/t/jobs/"> <span class="">Jobs</span> </a> <a class=" item active format " href="/t/tutorials/"> <span class="">Tutorials</span> </a> <a class=" item format " href="/t/"> <span class="">Tags</span> </a> <a class=" item format " href="/user/list/"> <span class="">Users</span> </a> </div> </span> <span class="phone-menus"> <div class="header item" id="logo"> <a href="/"><img class="ui image" width="220px" src="/static/transparent-logo.png"></a> </div> <div class="ui labeled icon attached fluid pointing menu" id="menu-header" style="background-color: white"> <div class="ui left simple dropdown item"> <i class="bars icon"><i class="dropdown icon"></i></i> <div class="menu"> <a class="item " href="/new/post/"> <i class=" edit icon"></i>New Post </a> <a class="item " href="/"> <i class=" list icon"></i> Latest </a> <a class="item " href="/t/news/"> <i class=" newspaper icon"></i> News </a> <a class="item " href="/t/jobs/"> <i class=" briefcase icon"></i> Jobs </a> <a class="item active " href="/t/tutorials/"> <i class=" info circle icon"></i> Tutorials </a> <a class="item " href="/t/"> <i class="tag icon"></i>Tags </a> <a class="item " href="/user/list/"> <i class=" world icon"></i> Users </a> </div> </div> <div class="ui right simple dropdown item"> </div> <div class="ui right simple dropdown item"> <i class="user icon"><i class="dropdown icon"></i></i> <div class="menu" id="login-opts"> <a class="item " href="/accounts/login/"><i class="sign-in icon"></i> Log In</a> <a class="item " href="/accounts/signup/"><i class="arrow circle up icon"></i> Sign Up</a> <a class="item " href="/info/about/"><i class="info circle icon"></i>About </a> </div> </div> </div> </span> <div class="ui bottom attached segment block"> <div class="ui stackable grid"> <div class="fit twelve wide content column"> <div class="ui horizontal basic top-menu segments"> <div class="ui horizontal basic top-menu segments"> <div style="padding-right: 19px;"> <div class="ui small compact menu sorting no-box-shadow"> <div class="ui simple dropdown item"> Limit <i class="dropdown icon"></i> <div class="menu"> <a class="item" href="/t/tutorials/?limit=all"> <i class="check icon"></i>all time </a> <a class="item" href="/t/tutorials/?limit=today"> <i class=""></i>today </a> <a class="item" href="/t/tutorials/?limit=week"> <i class=""></i>this week </a> <a class="item" href="/t/tutorials/?limit=month"> <i class=""></i>this month </a> <a class="item" href="/t/tutorials/?limit=year"> <i class=""></i>this year </a> <div class="ui divider"></div> <a class="item" href="/t/open/"> <i class=""></i>Unanswered </a> <a class="item" href="/"> <i class=""></i>All posts </a> </div> </div> </div> </div> <div style="padding-right: 19px;"> <div class="ui small compact menu sorting no-box-shadow"> <div class="ui simple dropdown item"> Sort <i class="dropdown icon"></i> <div class="menu"> <a class="item" href="/t/tutorials/?order=update"> <i class=""></i>Update </a> <a class="item" href="/t/tutorials/?order=answers"> <i class=""></i>Answers </a> <a class="item" href="/t/tutorials/?order=bookmarks"> <i class=""></i>Bookmarks </a> <a class="item" href="/t/tutorials/?order=creation"> <i class=""></i>Creation </a> <a class="item" href="/t/tutorials/?order=replies"> <i class=""></i>Replies </a> <a class="item" href="/t/tutorials/?order=rank"> <i class="check icon"></i>Rank </a> <a class="item" href="/t/tutorials/?order=views"> <i class=""></i>Views </a> <a class="item" href="/t/tutorials/?order=votes"> <i class=""></i>Votes </a> </div> </div> </div> </div> </div> <div class="ui basic segment search-bar" id="search-anchor"> <div class="center-text "> <form class="ui form" method="GET" action="/post/search/" style="margin: 0"> <div class="ui search"> <div class="ui icon input"> <input value="" class="search-input" type="text" name="query" placeholder="Search ... "> <i class="search icon"></i> </div> </div> </form> </div> </div> </div> <div class="ui divided items"> <div class="post open item" data-value="9157825"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>3.1k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/9157825/"> Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bioconductor/"> bioconductor </a> <a class="ptag" href="/tag/Install/"> Install </a> </div> <div class="right floated muted"> <span> 7 months ago <a href="/u/11519/"> BioinfGuru </a> ▴ 70 </span> </div> </div> </div> </div> <div class="post open item" data-value="9154016"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.5k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/9154016/"> Read data file containing both counts and annotation into edgeR </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/rpkm/"> rpkm </a> <a class="ptag" href="/tag/edgeR/"> edgeR </a> <a class="ptag" href="/tag/featureCounts/"> featureCounts </a> </div> <div class="right floated muted"> <span> 15 months ago <a href="/u/179/"> Gordon Smyth </a> <i class="ui muted bolt icon"></i> 52k </span> </div> </div> </div> </div> <div class="post open item" data-value="117436"> <div class="stats"> <div class="ui mini stat left label"> <div>17</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>9.8k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/117436/"> Updated Support Site Editor </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/support.bioconductor.org/"> support.bioconductor.org </a> <a class="ptag" href="/tag/editor/"> editor </a> <a class="ptag" href="/tag/markdown/"> markdown </a> <a class="ptag" href="/tag/updates/"> updates </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 8 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/77445/"> <span itemprop="name">Mj.A.</span> </a> • 0 • written 5.8 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/10588/"> <span itemprop="name">shepherl</span> </a> <i class="ui muted bolt icon"></i> 4.1k </div> </div> </div> </div> <div class="post open item" data-value="9149749"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>1.8k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/9149749/"> Online workshop "Working with ChatGPT in R" 2023-03-09 </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/chatgpt/"> chatgpt </a> <a class="ptag" href="/tag/programming/"> programming </a> </div> <div class="right floated muted"> updated 7 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/77580/"> <span itemprop="name">gptnederlands.nl</span> </a> • 0 • written 21 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/3550/"> <span itemprop="name">Wolfgang Huber</span> </a> ★ 13k </div> </div> </div> </div> <div class="post open item" data-value="68402"> <div class="stats"> <div class="ui mini stat left label"> <div>7</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>5</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>6.7k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/68402/"> Accessing Public Genomic Data from Bioconductor </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/geoquery/"> geoquery </a> <a class="ptag" href="/tag/geometadb/"> geometadb </a> <a class="ptag" href="/tag/sradb/"> sradb </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> written 9.5 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/490/"> <span itemprop="name">Sean Davis</span> </a> <i class="ui muted bolt icon"></i> 21k </div> </div> </div> </div> <div class="post open item" data-value="134743"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>2.6k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/134743/"> Mass Spectrometry Data Analysis with the Spectra Package </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/mass%20spectrometry/"> mass spectrometry </a> <a class="ptag" href="/tag/proteomics/"> proteomics </a> <a class="ptag" href="/tag/metabolomics/"> metabolomics </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> written 4.1 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/6987/"> <span itemprop="name">Johannes Rainer</span> </a> ★ 2.1k </div> </div> </div> </div> <div class="post open item" data-value="130708"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.9k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/130708/"> [LIBD rstats club] Bioconductor overview </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bioconductor/"> bioconductor </a> <a class="ptag" href="/tag/libdrstats/"> libdrstats </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 4.6 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/5645/"> <span itemprop="name">Laurent Gatto</span> </a> <i class="ui muted bolt icon"></i> 1.6k • written 4.6 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/6526/"> <span itemprop="name">Leonardo Collado Torres</span> </a> ★ 1.1k </div> </div> </div> </div> <div class="post open item" data-value="129969"> <div class="stats"> <div class="ui mini stat left label"> <div>4</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.4k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/129969/"> How to post Salmon data to GEO for use with tximeta </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/salmon/"> salmon </a> <a class="ptag" href="/tag/tximeta/"> tximeta </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 4.6 years ago <a href="/u/5822/"> Michael Love </a> <i class="ui muted bolt icon"></i> 43k </span> </div> </div> </div> </div> <div class="post open item" data-value="129447"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/129447/"> selecting result from deseq2 </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/deseq2/"> deseq2 </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 4.7 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/5822/"> <span itemprop="name">Michael Love</span> </a> <i class="ui muted bolt icon"></i> 43k • written 4.7 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/23201/"> <span itemprop="name">Nas 1989</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="122077"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>2.5k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/122077/"> Differential Methylation Analysis using ChAMP </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/champ/"> champ </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 5.4 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/13904/"> <span itemprop="name">Yuan Tian</span> </a> ▴ 290 • written 5.5 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/21072/"> <span itemprop="name">learning.iq84</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="120210"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>2.4k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/120210/"> How to download reference genomes using the RBioMart from ensembl? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/BioMart/"> BioMart </a> <a class="ptag" href="/tag/downloading%20reference%20genome/"> downloading reference genome </a> <a class="ptag" href="/tag/alignment/"> alignment </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 5.6 years ago <a href="/u/20563/"> jcollidelcs </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="118249"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.1k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/118249/"> Reading csv file in minfi </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/minfi/"> minfi </a> <a class="ptag" href="/tag/infinium%20450K/"> infinium 450K </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 5.8 years ago <a href="/u/16075/"> lalchungnungabt17 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="110298"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>2.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/110298/"> Update gene symbols in GeneSetCollection </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/gseabase/"> gseabase </a> <a class="ptag" href="/tag/msigdb/"> msigdb </a> <a class="ptag" href="/tag/genesetcollection/"> genesetcollection </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> written 6.4 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/6868/"> <span itemprop="name">t.kuilman</span> </a> ▴ 170 </div> </div> </div> </div> <div class="post open item" data-value="108664"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>3.6k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/108664/"> Importing multiple .h5 files using tximport </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/tximport/"> tximport </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 6.6 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/2771/"> <span itemprop="name">Steve Lianoglou</span> </a> ★ 13k • written 6.6 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/15764/"> <span itemprop="name">nelson.s.garcia</span> </a> ▴ 10 </div> </div> </div> </div> <div class="post open item" data-value="108194"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>6</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.9k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/108194/"> use deseq2 in asthma </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/deseq2/"> deseq2 </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 6.6 years ago <a href="/u/15652/"> krwyaong.ju </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="71905"> <div class="stats"> <div class="ui mini stat left label"> <div>21</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>10</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>9.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/71905/"> Bioconductor on Coursera </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/mooc/"> mooc </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 6.7 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/15326/"> <span itemprop="name">ifmrdatascience</span> </a> • 0 • written 9.2 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/2979/"> <span itemprop="name">Kasper Daniel Hansen</span> </a> ★ 6.5k </div> </div> </div> </div> <div class="post open item" data-value="105121"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>5</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>5.6k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/105121/"> Patch for GEOquery package error: getGEO Error in download.file, cannot open destfile </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/R/"> R </a> <a class="ptag" href="/tag/GEO/"> GEO </a> <a class="ptag" href="/tag/geoquery/"> geoquery </a> <a class="ptag" href="/tag/geoquery%20error%20message/"> geoquery error message </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 6.9 years ago <a href="/u/14839/"> martinguerrerog89 </a> ▴ 20 </span> </div> </div> </div> </div> <div class="post open item" data-value="98940"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.4k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/98940/"> Using Subversion to update /devel branch of Bioconductor package </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/subversion/"> subversion </a> <a class="ptag" href="/tag/bioc-devel/"> bioc-devel </a> <a class="ptag" href="/tag/package%20development/"> package development </a> <a class="ptag" href="/tag/usedevel/"> usedevel </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 7.3 years ago <a href="/u/9617/"> Bohdan Khomtchouk </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="98851"> <div class="stats"> <div class="ui mini stat left label"> <div>2</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>4.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/98851/"> BoF Bioc2017: Analyzing publicly available cancer genomics data from GTEx and TCGA with Bioconductor </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/public%20data/"> public data </a> <a class="ptag" href="/tag/TCGA/"> TCGA </a> <a class="ptag" href="/tag/GTEx/"> GTEx </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 7.3 years ago <a href="/u/10588/"> shepherl </a> <i class="ui muted bolt icon"></i> 4.1k </span> </div> </div> </div> </div> <div class="post open item" data-value="98844"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>3.3k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/98844/"> BoF Bioc2017: Infrastructure for efficient storage and processing of large-scale single-cell genomics data </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/single-cell/"> single-cell </a> <a class="ptag" href="/tag/objectstorage/"> objectstorage </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 7.3 years ago <a href="/u/10588/"> shepherl </a> <i class="ui muted bolt icon"></i> 4.1k </span> </div> </div> </div> </div> <div class="post open item" data-value="98536"> <div class="stats"> <div class="ui mini stat left label"> <div>6</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>3.5k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/98536/"> BoF "Writing papers in Rmarkdown, BiocStyle... (and books, posters)" </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/biocstyle/"> biocstyle </a> <a class="ptag" href="/tag/Rmarkdown/"> Rmarkdown </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 7.4 years ago <a href="/u/3550/"> Wolfgang Huber </a> ★ 13k </span> </div> </div> </div> </div> <div class="post open item" data-value="96195"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.6k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/96195/"> LEA won't run lfmm sequentially and independently on individual environmental variables when d set to 0 </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/LEA/"> LEA </a> <a class="ptag" href="/tag/%20lfmm/"> lfmm </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 7.5 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/7962/"> <span itemprop="name">eric.frichot</span> </a> • 0 • written 7.5 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/12964/"> <span itemprop="name">afreedman405</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="68039"> <div class="stats"> <div class="ui mini stat left label"> <div>8</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>4.8k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/68039/"> Epigenomics RoadMap Project files now accessible via AnnotationHub </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/AnnotationHub/"> AnnotationHub </a> <a class="ptag" href="/tag/Epigenomics/"> Epigenomics </a> <a class="ptag" href="/tag/BigData/"> BigData </a> <a class="ptag" href="/tag/RoadMap%20Project/"> RoadMap Project </a> <a class="ptag" href="/tag/NIH/"> NIH </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 7.6 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/12951/"> <span itemprop="name">vanesa_1230</span> </a> • 0 • written 9.5 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/6563/"> <span itemprop="name">Sonali Arora</span> </a> ▴ 390 </div> </div> </div> </div> <div class="post open item" data-value="92091"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>8</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>3.4k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/92091/"> "developing" with HDF5Array </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/hdf5/"> hdf5 </a> <a class="ptag" href="/tag/DelayedArray/"> DelayedArray </a> <a class="ptag" href="/tag/summarizedexperiment/"> summarizedexperiment </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 7.8 years ago <a href="/u/4/"> Vincent J. Carey, Jr. </a> <i class="ui muted bolt icon"></i> 6.7k </span> </div> </div> </div> </div> <div class="post open item" data-value="91770"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>8.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/91770/"> doParallel foreach already exporting variable(s) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/doParallel/"> doParallel </a> <a class="ptag" href="/tag/foreach/"> foreach </a> <a class="ptag" href="/tag/export/"> export </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 7.8 years ago <a href="/u/11037/"> solo7773 </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="86701"> <div class="stats"> <div class="ui mini stat left label"> <div>4</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>3.7k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/86701/"> Workflow for low-level analysis of single-cell RNA-seq data </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/scran/"> scran </a> <a class="ptag" href="/tag/scater/"> scater </a> <a class="ptag" href="/tag/single%20cell/"> single cell </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 8.3 years ago <a href="/u/6732/"> Aaron Lun </a> ★ 28k </span> </div> </div> </div> </div> <div class="post open item" data-value="80845"> <div class="stats"> <div class="ui mini stat left label"> <div>5</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>3.5k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/80845/"> Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/shortread/"> shortread </a> <a class="ptag" href="/tag/rsubread/"> rsubread </a> <a class="ptag" href="/tag/ensembldb/"> ensembldb </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 8.6 years ago <a href="/u/8324/"> phil.chapman </a> ▴ 150 </span> </div> </div> </div> </div> <div class="post open item" data-value="79529"> <div class="stats"> <div class="ui mini stat left label"> <div>7</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>4.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/79529/"> New edX "Data analysis for Life Sciences" module: High performance computing for reproducible genomics </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/annotation/"> annotation </a> <a class="ptag" href="/tag/genomicranges/"> genomicranges </a> <a class="ptag" href="/tag/visualization/"> visualization </a> <a class="ptag" href="/tag/docker/"> docker </a> <a class="ptag" href="/tag/shiny/"> shiny </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 8.7 years ago <a href="/u/4/"> Vincent J. Carey, Jr. </a> <i class="ui muted bolt icon"></i> 6.7k </span> </div> </div> </div> </div> <div class="post open item" data-value="70357"> <div class="stats"> <div class="ui mini stat left label"> <div>7</div> <div>votes</div> </div> <div class="ui label stat mini tutorial has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>7.4k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/70357/"> Course Material from BioC 2015: Where Software and Biology Connect </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bioc2015/"> bioc2015 </a> <a class="ptag" href="/tag/course-material/"> course-material </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> updated 9.4 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/4256/"> <span itemprop="name">Dan Tenenbaum</span> </a> ★ 8.2k • written 9.4 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/6563/"> <span itemprop="name">Sonali Arora</span> </a> ▴ 390 </div> </div> </div> </div> <div class="post open item" data-value="69677"> <div class="stats"> <div class="ui mini stat left label"> <div>11</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>6.1k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/69677/"> Introduction to Bioconductor for high-throughput sequence analysis </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/GenomicRanges/"> GenomicRanges </a> <a class="ptag" href="/tag/Annotation/"> Annotation </a> <a class="ptag" href="/tag/RNAseq/"> RNAseq </a> <a class="ptag" href="/tag/visualization/"> visualization </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 9.4 years ago <a href="/u/1513/"> Martin Morgan </a> <i class="ui muted bolt icon"></i> 25k </span> </div> </div> </div> </div> <div class="post open item" data-value="69411"> <div class="stats"> <div class="ui mini stat left label"> <div>6</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>4.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/69411/"> Orchestrating a small, parallel, RNA-seq pre-processing workflow using R </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/rnaseq/"> rnaseq </a> <a class="ptag" href="/tag/biocparallel/"> biocparallel </a> <a class="ptag" href="/tag/workflows/"> workflows </a> <a class="ptag" href="/tag/sra/"> sra </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 9.4 years ago <a href="/u/490/"> Sean Davis </a> <i class="ui muted bolt icon"></i> 21k </span> </div> </div> </div> </div> <div class="post open item" data-value="69329"> <div class="stats"> <div class="ui mini stat left label"> <div>8</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>3.8k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/69329/"> Statistics and Computing in Genome Science (CSAMA) Course Material </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/rnaseq/"> rnaseq </a> <a class="ptag" href="/tag/chipseq/"> chipseq </a> <a class="ptag" href="/tag/visualization/"> visualization </a> <a class="ptag" href="/tag/metagenomics/"> metagenomics </a> <a class="ptag" href="/tag/proteomics/"> proteomics </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 9.4 years ago <a href="/u/1513/"> Martin Morgan </a> <i class="ui muted bolt icon"></i> 25k </span> </div> </div> </div> </div> <div class="post open item" data-value="68404"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini tutorial open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>4.1k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tutorial: <a href="/p/68404/"> dplyr and the GEOmetadb package for mining NCBI GEO metadata </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/geometadb/"> geometadb </a> <a class="ptag" href="/tag/dplyr/"> dplyr </a> <a class="ptag" href="/tag/Tutorial/"> Tutorial </a> </div> <div class="right floated muted"> <span> 9.5 years ago <a href="/u/490/"> Sean Davis </a> <i class="ui muted bolt icon"></i> 21k </span> </div> </div> </div> </div> </div> <div class="ui page-bar segment"> <span class="phone">33 results • Page </span> 1 of 1 </div> </div> <div class="four wide column sidefeed"> <div class="ui large wrap-text" id="sidebar"> <b>Recent ... </b> <div class="ui large wrap-text"> <div class="event"> <div class="ui container"> <span>Replies </span> <div class="ui relaxed list" > <div class="item spaced"> <a href="/p/9160725/"> Comment: What type of counts data to import for performing Isoform analysis in edgeR</a> by <a href="/u/17679/">mohammedtoufiq91 </a> <span> ▴ 10 </span> <div class="muted" style=""> @gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you. </div> </div> <div class="item spaced"> <a href="/p/9160724/"> Comment: Differential Expression Genes as Independent Variables</a> by <a href="/u/179/">Gordon Smyth </a> <span> <i class="ui muted bolt icon"></i> 52k </span> <div class="muted" style=""> Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible. </div> </div> <div class="item spaced"> <a href="/p/9160723/"> Comment: Differential Expression Genes as Independent Variables</a> by <a href="/u/78908/">abadgerw </a> <span> • 0 </span> <div class="muted" style=""> The data that is repeated is a quantitative metric of post-mortem pathology across multiple sections. Not all patients have the same number… </div> </div> <div class="item spaced"> <a href="/p/9160722/"> Answer: Crossover design with limma</a> by <a href="/u/179/">Gordon Smyth </a> <span> <i class="ui muted bolt icon"></i> 52k </span> <div class="muted" style=""> Your experiment is somewhat more elaborate than a classical crossover design because of the period-specific baseline controls. The analyses… </div> </div> <div class="item spaced"> <a href="/p/9160721/"> Answer: Differential Expression Genes as Independent Variables</a> by <a href="/u/179/">Gordon Smyth </a> <span> <i class="ui muted bolt icon"></i> 52k </span> <div class="muted" style=""> Sorry, your question doesn't make sense to me. There are tens of thousands of genes and you can't run a mixed model analysis with one depen… </div> </div> </div> </div> </div> <div class="ui divider"></div> <div class="event"> <div class="ui container"> <div>Votes </div> <div class="ui relaxed list" > <div class="item spaced" > <a href="/p/9160720/">Comment: What type of counts data to import for performing Isoform analysis in edgeR</a> </div> <div class="item spaced" > <a href="/p/9160716/">Answer: What type of counts data to import for performing Isoform analysis in edgeR</a> </div> <div class="item spaced" > <a href="/p/133308/">Transcript-level differential expression using DESeq2</a> </div> <div class="item spaced" > <a href="/p/9160714/">Comment: What type of counts data to import for performing Isoform analysis in edgeR</a> </div> <div class="item spaced" > <a href="/p/9160708/">Answer: What type of counts data to import for performing Isoform analysis in edgeR</a> </div> </div> </div> </div> <div class="ui divider"></div> <div class="event"> <div class="ui container"> <span>Awards</span> <a href="/b/list/"> • All <i class="ui angle small double right icon"></i></a> <div class="ui relaxed list" > <div class="item" style=""> <span> <a href="/b/view/popular-question/">Popular Question <i class="eye icon"></i></a> to <a href="/u/5916/"> Dario Strbenac</a> <span> ★ 1.5k </span> </span> </div> <div class="item" style=""> <span> <a href="/b/view/popular-question/">Popular Question <i class="eye icon"></i></a> to <a href="/u/7369/"> Marek Gierlinski</a> <span> ▴ 30 </span> </span> </div> <div class="item" style=""> <span> <a href="/b/view/scholar/">Scholar <i class="check circle outline icon"></i></a> to <a href="/u/179/"> Gordon Smyth</a> <span> <i class="ui muted bolt icon"></i> 52k </span> </span> </div> <div class="item" style=""> <span> <a href="/b/view/popular-question/">Popular Question <i class="eye icon"></i></a> to <a href="/u/17679/"> mohammedtoufiq91</a> <span> ▴ 10 </span> </span> </div> <div class="item" style=""> <span> <a href="/b/view/popular-question/">Popular Question <i class="eye icon"></i></a> to <a href="/u/1945/"> Hans-Ulrich Klein</a> <span> ▴ 330 </span> </span> </div> </div> </div> </div> <div class="ui divider"></div> <div class="event"> <div class="ui container"> <span>Locations</span> <a href="/user/list/">• All <i class="ui angle small double right icon"></i></a> <div class="ui relaxed list" > <div class="item spaced" > <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/6732/"> <img src="https://secure.gravatar.com/avatar/b1d9b3de6fc5202485c7a398f15ab399?s=90&d=retro"> </a> </span> The city by the bay, <span class="muted">8 minutes ago</span> </div> <div class="item spaced" > <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/3224/"> <img src="https://secure.gravatar.com/avatar/2edd996ca9e08fa9e0e517cf750c26af?s=90&d=retro"> </a> </span> UPF, Barcelona, Spain, <span class="muted">37 minutes ago</span> </div> <div class="item spaced" > <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/77544/"> <img src="https://secure.gravatar.com/avatar/06be279f3b96870ad1d8342320e92521?s=90&d=mp"> </a> </span> France, <span class="muted">53 minutes ago</span> </div> <div class="item spaced" > <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/78908/"> <img src="https://secure.gravatar.com/avatar/cfab3db98b514e128cbef4704f5ddb68?s=90&d=mp"> </a> </span> United Kingdom, <span class="muted">1 hour ago</span> </div> <div class="item spaced" > <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/64678/"> <img src="https://secure.gravatar.com/avatar/7405efbf5e06b5d9ad7812811f47ad47?s=90&d=mp"> </a> </span> United States, <span class="muted">2 hours ago</span> </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 521 users visited in the last hour</div> </div> <div class="ui three center aligned column stackable tiny grid"> <div class=" left aligned column" style="padding-right: 13%"> <b>Content</b> <a href="/#search-anchor">Search</a><br> <a href="/user/list/">Users</a><br> <a href="/t/">Tags</a><br> <a href="/b/list/">Badges</a> </div> <div class="left aligned column" style="padding-right: 12%"> <b>Help</b> <a href="/info/about/">About</a><br> <a href="/info/faq/">FAQ</a><br> </div> <div class=" left aligned column"> <b>Access</b> <a href="/info/rss/">RSS</a><br> <a href="/info/api/">API</a><br> <a href="#">Stats</a> </div> </div> <div class="ui divider"></div> <div class="ui vertical center aligned basic segment"> <p>Use of this site constitutes acceptance of our <a href="/info/policy/">User Agreement and Privacy Policy</a>.</p> <div class="smaller muted"> Powered by the <a href="https://github.com/ialbert/biostar-central" class="ui image"> <img src="/static/images/badge-forum.svg"></a> version 2.3.6 </div> </div> </div> </body> </html>