Showing : RNASEQ • reset
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50
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Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 15 hours ago by ★ 2.1k • written 16 hours ago by • 0
2
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10
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251
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edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 4 days ago by 47k • written 8 days ago by • 0
2
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2
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147
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Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
27 days ago • updated 17 days ago SciencyUsagi ▴ 10
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1
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145
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 22 days ago by 39k • written 25 days ago by • 0
3
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3
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165
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 23 days ago by 47k • written 23 days ago by • 0
0
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3
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176
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Gene TPM validity with STAR only quantification
RNASeq
written 5 weeks ago by ▴ 10
2
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5
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218
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Create the design matrix
DEGseq edgeR RNASeq
5 weeks ago Mohammad • 0
2
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4
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292
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How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
5 weeks ago mohammedtoufiq91 ▴ 10
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3
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162
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DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 6 weeks ago by 39k • written 6 weeks ago by • 0
0
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0
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85
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A problem with Experimental Design for Limma
limma RNASeq
7 weeks ago ToReality • 0
0
votes
3
replies
251
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Unusual MA and volcano plots?
DESeq2 RNASeq
written 7 weeks ago by ▴ 10
0
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1
reply
118
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Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 8 weeks ago by ★ 2.0k
1
vote
2
replies
163
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
8 weeks ago mohammedtoufiq91 ▴ 10
0
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0
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95
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RNA seq analysis
RNASeq
9 weeks ago lesseyl • 0
2
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3
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291
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Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
9 weeks ago mohammedtoufiq91 ▴ 10
0
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1
reply
109
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TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 9 weeks ago by ★ 2.1k • written 9 weeks ago by • 0
2
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4
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374
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Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
9 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
183
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 9 weeks ago by 39k • written 12 weeks ago by ▴ 10
1
vote
1
reply
182
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 10 weeks ago by 47k • written 10 weeks ago by • 0
0
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3
replies
233
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
updated 10 weeks ago by • 0 • written 10 weeks ago by • 0
1
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2
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194
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
11 weeks ago • updated 10 weeks ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
133
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Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 11 weeks ago by ★ 2.1k • written 11 weeks ago by • 0
0
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0
replies
98
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
11 weeks ago whduke • 0
0
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1
reply
127
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 11 weeks ago by 47k • written 11 weeks ago by • 0
0
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3
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170
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Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 11 weeks ago by 62k • written 11 weeks ago by • 0
0
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1
reply
135
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Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 12 weeks ago by ★ 1.2k • written 12 weeks ago by • 0
2
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3
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191
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Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 12 weeks ago by 47k • written 12 weeks ago by • 0
0
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2
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215
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RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 3 months ago by 39k • written 3 months ago by • 0
3
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7
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466
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3 months ago by 47k • written 3 months ago by • 0
1
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2
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206
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Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3 months ago by ★ 1.2k • written 3 months ago by • 0
0
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0
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98
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3 months ago rridley3 • 0
3
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15
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754
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Atena package - error (new user)
RNAseq R Atena
updated 21 hours ago by ▴ 30 • written 3 months ago by • 0
2
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5
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1.6k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3 months ago by 39k • written 19 months ago by • 0
0
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1
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296
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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 4 months ago by 62k • written 4 months ago by • 0
0
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0
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129
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question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
4 months ago snowmattin • 0
0
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0
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126
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
4 months ago Julieta • 0
0
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0
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130
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Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
4 months ago estafana.t98 • 0
3
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4
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315
views
difference between txi$counts and txi$abundance when countsFromAbundance is true
RNAseq tximport
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
0
votes
1
reply
172
views
Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 4 months ago by ★ 2.1k • written 4 months ago by • 0
0
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1
reply
216
views
Reversing DEseq2 normalization
DESeq2 Normalization RNASeq
updated 4 months ago by 39k • written 5 months ago by • 0
0
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0
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132
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
4 months ago marymshahi2021 • 0
0
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2
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1.4k
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maSigPro: how to extract the genes in the same cluster
rnaseq
updated 5 months ago by • 0 • written 6.8 years ago by ▴ 10
1
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2
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235
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how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 5 months ago by ★ 2.1k • written 5 months ago by • 0
0
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1
reply
218
views
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 5 months ago by 39k • written 5 months ago by • 0
2
votes
7
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469
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
updated 5 months ago by ▴ 120 • written 5 months ago by ▴ 10
0
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2
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413
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 5 months ago by ▴ 220 • written 7 months ago by • 0
0
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0
replies
147
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DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
5 months ago osieman52 • 0
4
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5
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659
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Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 5 months ago by 39k • written 6 months ago by • 0
1
vote
1
reply
177
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Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 6 months ago by ★ 2.1k • written 6 months ago by • 0
1
vote
5
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505
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 6 months ago by 39k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: struggling to create a heatmap by ATpoint ★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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