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"> <i class="search icon"></i> </div> </div> </form> </div> </div> </div> <div class="ui blue filter message"> Showing : <code>pseudobulk</code> • <a href="/t/"> reset <i class="undo small icon"></i> </a> </div> <div class="ui divided items"> <div class="post open item" data-value="9161351"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>81</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9161351/"> How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/SingleCellData/"> SingleCellData </a> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> <a class="ptag" href="/tag/pseudobulk/"> pseudobulk </a> <a class="ptag" href="/tag/sing/"> sing </a> </div> <div class="right floated muted"> updated 6 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/5106/"> <span itemprop="name">James W. MacDonald</span> </a> <i class="ui muted bolt icon"></i> 68k • written 8 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/56132/"> <span itemprop="name">Sara_Ald</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9156959"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>5</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"> <a href="/p/9156959/"> Right way to pseudobulk donors across replicates in edgeR </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/pseudobulk/"> pseudobulk </a> <a class="ptag" href="/tag/edgeR/"> edgeR </a> <a class="ptag" href="/tag/DifferentialExpression/"> DifferentialExpression </a> </div> <div class="right floated muted"> updated 8 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/78028/"> <span itemprop="name">Reza Ghamsari</span> </a> • 0 • written 11 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/58703/"> <span itemprop="name">Jack S.</span> </a> ▴ 60 </div> </div> </div> </div> <div class="post open item" data-value="9158511"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>786</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9158511/"> How to add Ensembl ids after Pseudobulk analysis by DESeq2 </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Seurat/"> Seurat </a> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> <a class="ptag" href="/tag/single-cell/"> single-cell </a> <a class="ptag" href="/tag/scRNA/"> scRNA </a> <a class="ptag" href="/tag/Pseudobulk/"> Pseudobulk </a> </div> <div class="right floated muted"> updated 9 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/2020/"> <span itemprop="name">Guido Hooiveld</span> </a> ★ 4.1k • written 9 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/56132/"> <span itemprop="name">Sara_Ald</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9156610"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>1.3k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9156610/"> Pseudobulk-DESeq2 analyze multiple cell types at once? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/pseudobulk/"> pseudobulk </a> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> </div> <div class="right floated muted"> updated 12 months 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 12 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/77114/"> <span itemprop="name">puffsquash</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9155715"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>5</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.7k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9155715/"> scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/pseudobulk/"> pseudobulk </a> <a class="ptag" href="/tag/seurat/"> seurat </a> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> </div> <div class="right floated muted"> updated 14 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/16406/"> <span itemprop="name">Kevin Blighe</span> </a> ★ 4.0k • written 14 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/71895/"> <span itemprop="name">daiane.hemerichbrennan</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9150812"> <div class="stats"> <div class="ui mini stat left label"> <div>2</div> <div>votes</div> </div> <div class="ui label stat mini question open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9150812/"> How to aggregate pseudobulks: Normalization & Log-Transformation </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/pseudobulk/"> pseudobulk </a> <a class="ptag" href="/tag/scRNAseq/"> scRNAseq </a> <a class="ptag" href="/tag/GSVA/"> GSVA </a> </div> <div class="right floated muted"> <span> 22 months ago <a href="/u/62204/"> Tadeoye </a> ▴ 20 </span> </div> </div> </div> </div> <div class="post open item" data-value="9148606"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9148606/"> Tissue Level Differential Expression Analysis </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> <a class="ptag" href="/tag/DifferentialExpression/"> DifferentialExpression </a> <a class="ptag" href="/tag/differentialex/"> differentialex </a> <a class="ptag" href="/tag/Pseudobulk/"> Pseudobulk </a> <a class="ptag" href="/tag/SingleCell/"> SingleCell </a> </div> <div class="right floated muted"> updated 2.2 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 2.2 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/57419/"> <span itemprop="name">skanda.hebbale</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9145642"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>2</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"> <a href="/p/9145642/"> DESeq2 aggregated single cell data </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/pseudobulk/"> pseudobulk </a> <a class="ptag" href="/tag/SingleCell/"> SingleCell </a> <a class="ptag" href="/tag/DESeq2/"> DESeq2 </a> </div> <div class="right floated muted"> <span> 2.6 years ago <a href="/u/34771/"> fluentin44 </a> • 0 </span> </div> </div> </div> </div> </div> <div class="ui page-bar segment"> <span class="phone">8 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/9161354/"> Comment: Error in retrieving clinical data</a> by <a href="/u/79621/">boidnoid </a> <span> • 0 </span> <div class="muted" style=""> I was having the same problem. You can check the answer in a [previous post][1]. Specifically, reinstalling the devel version from GitHub … </div> </div> <div class="item spaced"> <a href="/p/9161353/"> Answer: How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differenti</a> by <a href="/u/5106/">James W. MacDonald </a> <span> <i class="ui muted bolt icon"></i> 68k </span> <div class="muted" style=""> The short answer is yes. When you compute pseudo-bulk estimates, the counts/gene are expected to be somewhat proportional to the number of … </div> </div> <div class="item spaced"> <a href="/p/9161352/"> Comment: displaying the differential expression with deseq2 over 4X2 samples with the in</a> by <a href="/u/79619/">Leonard </a> <span> • 0 </span> <div class="muted" style=""> Visualize subject contributions to overall differential expression using: Volcano plots/scatter plots (subject-colored). Heatmaps (subject… </div> </div> <div class="item spaced"> <a href="/p/9161350/"> Comment: Plot title for PCA in DESeq2</a> by <a href="/u/78232/">AL </a> <span> • 0 </span> <div class="muted" style=""> Thank you! </div> </div> <div class="item spaced"> <a href="/p/9161349/"> Answer: Interpreting DESEQ2 interaction term and inclusion of covariate</a> by <a href="/u/14086/">swbarnes2 </a> <span> ★ 1.4k </span> <div class="muted" style=""> "ecotypehigh.rearing_high" will basically do a 4 group comparison, and tell you if any genes that change going from high to low change diff… </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/9161347/">Interpreting DESEQ2 interaction term and inclusion of covariate</a> </div> <div class="item spaced" > <a href="/p/112072/">A: Seurat/DESeq2 - single cell RNA-seq differential expression</a> </div> <div class="item spaced" > <a href="/p/9161339/">Answer: Plot title for PCA in DESeq2</a> </div> <div class="item spaced" > <a href="/p/60441/">A: DESeq2: detect significantly increasing across an ordinal variable</a> </div> <div class="item spaced" > <a href="/p/9161345/">Answer: DEseq2 design for additive treatment</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/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/5106/"> James W. 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