Showing : DESEq2 • reset
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DESeq2 design with continuous variables AND filtering of low counts
DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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4
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1.6k
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DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 3.0 years ago by ★ 5.2k • written 3.1 years ago by ▴ 670
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12
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3.8k
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t.test to determine the P-value in DESeq2
DESeq2
written 3.1 years ago by • 0
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3
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2.6k
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How to convert transcript counts to gene counts in R?
DESeq2 tximport
updated 7 months ago by • 0 • written 3.1 years ago by ▴ 50
2
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2
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3.0k
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Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed while using DESeq2
DESeq2
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
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2
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2.4k
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Cannot install bioconductor DESeq2 package on M1 mac ... any advice?
DESeq2 Install r
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
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8
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1.7k
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disappearing of DEGs genes by adjusting P-value < 0.05
DESeq2
3.1 years ago Maryam.sed1400 • 0
2
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2
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1.1k
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Second covariate
DESeq2
3.1 years ago liberios ▴ 10
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7
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1.7k
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statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 3.0 years ago by • 0 • written 3.1 years ago by ▴ 670
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1
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1.1k
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DESeq2 - Differential expression for miRNA data
DESeq2
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
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2
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1.1k
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Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
3.1 years ago Yijing • 0
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4
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1.9k
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Skew of differentially expressed genes using DESeq2
DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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2
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1.3k
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How to do differential gene expression analysis of very highly sparsed single cell data?
DESeq2
3.1 years ago Subhasis • 0
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2
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1.9k
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dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2 salmon
3.1 years ago manduchi ▴ 10
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5
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1.5k
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Running DESeq2 on viral infection without control/host data
DESeq2 viral controls
3.1 years ago f99942 • 0
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2
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1.2k
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Unexpectedly low number of DE genes?
DESeq2
3.1 years ago mhalache • 0
0
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2
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908
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RNA-seq DESeq2 factor design
DESeq2
3.1 years ago Grace • 0
0
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1
reply
4.3k
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Heatmap with result DESeq analysis
DESeq2 results Heatmaps plots
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
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20
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6.6k
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Deseq2 installed, but there is no package called ‘Biostrings’
DESeq2 Install
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
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1
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2.5k
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bigwig to counts
DESeq2 edgeR bigwig limma
3.1 years ago • updated 2.9 years ago Bogdan ▴ 670
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5
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4.6k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.1 years ago by 43k • written 4.4 years ago by • 0
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1
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1.6k
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I have problems installing DESeq2 using R4.1.2. It tells me that it is not available for my version of R and I need to upgrade my R version. but I ca…
DESeq2
updated 3.1 years ago by 4.2k • written 3.1 years ago by • 0
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4
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1.5k
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DESeq2 for ribo-IP analysis
DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
3
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1
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1.4k
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Identifying DEGs using lfcshrink()
DESeq2 lfcshrink
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 20
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4
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1.4k
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Is there a way to identify constituently expressed genes (not differentially expressed)?
DESeq2
3.1 years ago nute11a ▴ 10
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2
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1.5k
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Combine scRNAseq data for bulk analysis using DESeq2
DESeq2 scRNAseq Fluidigm
3.1 years ago evocanres • 0
3
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10
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3.1k
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Fold Change calculation when Batch Effect is present in RNA-seq data (DEseq2)
DESeq2 BatchEffect fold
3.1 years ago eve.olszanowski • 0
2
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1
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1.8k
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Correcting for all the comparisons that have been made in analysis
DESeq2 comparisons correction
updated 3.1 years ago by 68k • written 3.2 years ago by • 0
3
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4
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1.9k
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I have problems installing DESeq2 using R4.1.2. It tells me that it is not available for my version of R and I need to upgrade my R version. but I ca…
DESeq2
3.2 years ago • updated 3.1 years ago yari.hadi • 0
1
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2
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1.2k
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Modelling batch effect in DESeq2 - how to interpret the results?
DESeq2 BatchEffect
3.2 years ago annamariabugaj ▴ 10
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2.9k
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Unable to load data "pasillaGenes" in R because DESeq is not installed?
DESeq2 pasillaGenes
updated 3.2 years ago by 68k • written 4.9 years ago by • 0
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Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2 RNAseq bulk DifferentialExpression
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
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1
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1.1k
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Downloading DESeq package manually
DESeq2 Install
updated 3.2 years ago by ▴ 780 • written 3.2 years ago by • 0
1
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3
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9.2k
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DESeq2 - Error: full model matrix is less than full rank
microbiome DESeq2
updated 3.2 years ago by ▴ 40 • written 5.1 years ago by • 0
0
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1
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833
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Extracting multi-design adjusted counts on DESeq2
DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
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1
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1.1k
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DIfferentially abundant taxa but some of them are not present in both groups (DESeq2)
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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1
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982
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DESEQ2 time series with multiple variables
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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1
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1.0k
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Time serious analysis Wald test in results()
DESeq2 TimeSeriesExperiment
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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2.9k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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6
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2.9k
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No differentially expressed genes after DESeq
DESeq2 R
3.2 years ago Zach • 0
3
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7
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2.9k
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Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2 limma
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by ▴ 50
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4
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6.7k
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Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2 log2FC
3.2 years ago User000 • 0
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5
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1.9k
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DESEQ2 several samples per individual
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 50
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1
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1.3k
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Comparison between treatment timepoints in a single timeseries (control is first timepoint)
DESeq2 single-timeseries TimeSeriesExperiment
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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1
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1.2k
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Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
1
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1
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920
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Contrasts in Deseq2
DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
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5
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3.2k
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Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
3.2 years ago • updated 3.1 years ago marinaw ▴ 20
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895
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interaction term formula for DESEQ2?
DESeq2
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
0
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1
reply
538
views
Bioconductor Rpackages install
DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
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2
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875
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Do we need to correct any of the data from DESeq2, if we only want to investigate some of the comparisons?
DESeq2 correction
3.2 years ago smac_head • 0
4,839 results • Page 18 of 97
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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