Showing : rnaseq • reset
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Using featureCounts and downloading Rsubread
Rsubread featureCounts DESeq2 R RNASeq
17 minutes ago • updated 11 minutes ago margo • 0
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146
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Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
updated 5 days ago by • 0 • written 13 days ago by • 0
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2
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82
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How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 6 days ago by 36k • written 6 days ago by • 0
3
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11
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352
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RNA-seq: compare two technical replicates
RNASeq
updated 14 days ago by 45k • written 20 days ago by • 0
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9
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805
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Deseq2 normalization for WGCNA
RNASeq Deseq2 DESeq2 WGCNA
updated 16 days ago by 36k • written 4 months ago by • 0
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2
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101
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edgeR
rnaseq edgeR
updated 27 days ago by 45k • written 27 days ago by • 0
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5
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4.6k
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EDGE-R exact test vs QL F-test
edger rnaseq
updated 28 days ago by • 0 • written 5.9 years ago by ▴ 20
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3
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133
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Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 28 days ago by ★ 1.0k • written 29 days ago by • 0
5
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6
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239
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Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
4 weeks ago Alan • 0
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70
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Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
4 weeks ago chiwut.wong • 0
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7
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285
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DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 5 weeks ago by 36k • written 5 weeks ago by • 0
5
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13
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2.7k
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Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 5 weeks ago by • 0 • written 4.9 years ago by ▴ 10
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63
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
5 weeks ago OST • 0
2
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4
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163
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confused with tximport counts abundance using salmon input
RNASeq tximport
5 weeks ago Al90 • 0
4
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4
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830
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 6 weeks ago by • 0 • written 8 months ago by • 0
3
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3
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6.0k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 6 weeks ago by 36k • written 5.8 years ago by ▴ 10
0
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1
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140
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Rtracklayer
rtracklayer RNASeq gff
updated 6 weeks ago by 59k • written 6 weeks ago by • 0
0
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1
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122
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Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 6 weeks ago by 36k • written 6 weeks ago by • 0
1
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4
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634
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Issues with scaling down enrichplot's dotplot and gseaplot2 plots
RNASeq clusterProfiler enrichplot
updated 6 weeks ago by • 0 • written 10 months ago by • 0
0
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3
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145
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DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 7 weeks ago by 36k • written 7 weeks ago by • 0
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2
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1.7k
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DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 7 weeks ago by • 0 • written 5.7 years ago by ▴ 40
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2
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3.1k
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deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 7 weeks ago by • 0 • written 4.7 years ago by • 0
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82
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How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
7 weeks ago treebig44 ▴ 30
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4
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219
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limma: Genes Associated with Continuous Predictor in Subsets of Samples
RNASeq limma
8 weeks ago • updated 7 weeks ago danphillips28 • 0
1
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0
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83
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Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery RNASeq
7 weeks ago Liliian • 0
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0
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85
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Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
7 weeks ago Raito92 ▴ 60
2
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2
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123
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Make samples symbols bigger in PCA / MDS analysis with plotMDS function
plotMDS PCA RNASeq MDS
updated 7 weeks ago by 45k • written 8 weeks ago by ▴ 60
0
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1
reply
137
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GSEA using custom GO annotations
RNASeq GSEA
updated 8 weeks ago by ★ 2.8k • written 8 weeks ago by • 0
0
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1
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125
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Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 8 weeks ago by 45k • written 8 weeks ago by • 0
4
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1
reply
167
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Finding significant up-regulated and down-regulated genes given a log2FoldChange threshold
DESeq2 RNASeq RNASeqData
updated 8 weeks ago by 36k • written 8 weeks ago by ▴ 30
1
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1
reply
102
views
Strange error while running DESeq() function.
DESeq2 RNASeq RNASeqData
updated 8 weeks ago by 36k • written 8 weeks ago by ▴ 30
2
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6
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249
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How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
9 weeks ago treebig44 ▴ 30
0
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0
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94
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 9 weeks ago by 36k • written 9 weeks ago by • 0
2
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2
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178
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Complex contrasts in limma
RNASeq limma DifferentialExpression
10 weeks ago tcalvo ▴ 70
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3
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339
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EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 10 weeks ago by 45k • written 9 months ago by ▴ 360
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5
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3.9k
views
limma-voom
RNASeq Normalization limma edgeR RNASeq Normalization limma edgeR
updated 10 weeks ago by 45k • written 8.3 years ago by ▴ 360
2
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6
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1.3k
views
Three way-interaction on voom (limma) data, including a factor with > 2 levels
RNASeq limma voom anova
updated 10 weeks ago by ▴ 70 • written 4.9 years ago by ▴ 70
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2
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197
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Differential expression in fixed windows
DESeq2 RNASeq
12 weeks ago • updated 11 weeks ago anatmela • 0
2
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1
reply
187
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DESeq2 handling of replicates
DESeq2 RNASeq limma
updated 12 weeks ago by 36k • written 12 weeks ago by • 0
0
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1
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140
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Controlling for sex variance in Galaxy DESeq2
DESeq2 RNASeq Galaxy
updated 3 months ago by 36k • written 3 months ago by • 0
0
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1
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165
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95% Confidence intervals for Fold Changes computed by DESeq2
DESeq2 RNASeq
updated 3 months ago by ★ 1.2k • written 3 months ago by • 0
10
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3
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387
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lfcShrink function for different comparison
DESeq2 RNASeq
updated 3 months ago by ▴ 20 • written 18 months ago by ▴ 50
0
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6
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395
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Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3 months ago by 36k • written 3 months ago by ▴ 60
0
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1
reply
168
views
Exporting org.*.*.db Gene Ontology annotations to excel sheet or txt
OrgDb RNASeq
updated 3 months ago by 59k • written 3 months ago by • 0
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4
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329
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How do you get averages of each group in Limma output
RNASeq limma
3 months ago Matthew • 0
0
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4
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315
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Multi-factor paired RNAseq differential analysis with DEseq2
DESeq2 RNASeq
updated 3 months ago by ★ 1.0k • written 3 months ago by • 0
3
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9
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1.4k
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LOC gene IDs for characterised genes in annotation files
Annotation RNAseq
updated 3 months ago by • 0 • written 12 months ago by • 0
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3
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314
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DESeq2 contrast multiple treated conditions versus multiple control conditions
RNASeq DESeq2
updated 3 months ago by ▴ 280 • written 3 months ago by • 0
0
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3
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394
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using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3 months ago by 45k • written 3 months ago by ▴ 70
1
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2
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173
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Correct use of Likelihood Ratio Test and LFC Shrinkage
RNASeq LRT DESeq2 lfcShrink
updated 3 months ago by 36k • written 3 months ago by • 0
50 results • Page 1 of 1
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Answer: Using featureCounts and downloading Rsubread by James W. MacDonald 59k
You need to tell `BiocManager;;install` that you want to install the `Rsubread` package. ``` BiocManager::install("Rsubread") library(…
Comment: featureCounts: 0% successfully assigned fragments by KMS • 0
Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% s…
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene by James W. MacDonald 59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma by AyHi • 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files by lesefo6448 • 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
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Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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