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Showing :
RNA-seq
•
reset
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 5.9 years ago by
aishu.jp
▴ 30
1
vote
6
replies
931
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 4 weeks ago by
Michael Love
43k • written 4 weeks ago by
nramakr
▴ 10
0
votes
2
replies
287
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
9 weeks ago
paul.meraner
• 0
0
votes
0
replies
197
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis
genomes
RNA-Seq
co-expression
wgcna
11 weeks ago
Fernanda
• 0
1
vote
3
replies
566
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 6 months ago by
James W. MacDonald
67k • written 6 months ago by
Ben
▴ 50
2
votes
4
replies
670
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 6 months ago by
Michael Love
43k • written 6 months ago by
shaunpeterson
• 0
1
vote
2
replies
628
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq
duplicateCorrelation
limma
voom
7 months ago
Dylan.Sheerin
• 0
2
votes
5
replies
980
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 5 months ago by
ATpoint
★ 4.6k • written 7 months ago by
Reza
• 0
3
votes
3
replies
908
views
permutation test in edgeR
rna-seq
edgeR
updated 7 months ago by
Gordon Smyth
52k • written 8 months ago by
Netanel
• 0
0
votes
1
reply
1.1k
views
Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 12 months ago by
ATpoint
★ 4.6k • written 6.7 years ago by
saad_k6
• 0
0
votes
2
replies
530
views
WGCNA less samples
RNA-Seq
WGCNA
Worms
12 months ago
davca
• 0
0
votes
4
replies
1.1k
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
14 months ago
ar14g12
• 0
0
votes
2
replies
4.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 4.4 years ago by
Arindam
▴ 80
2
votes
3
replies
3.3k
views
TPM from STAR mapped counts
GeneExpression
GenomicFeatures
RNA-Seq
TPM
updated 15 months ago by
Gordon Smyth
52k • written 15 months ago by
gingergeiger22
• 0
0
votes
3
replies
971
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq
RNA-seq
DESeq2
updated 15 months ago by
Alejandro Reyes
★ 1.9k • written 15 months ago by
Alice
• 0
3
votes
4
replies
1.3k
views
lfcShrink() and batch effects in DESeq2
BatchEffect
lfcshrink
RNA-seq
DESeq2
16 months ago
Eva
▴ 10
0
votes
3
replies
914
views
Fishpond with unbalanced dataset
rna-seq
salmon
fishpond
swish
updated 18 months ago by
Michael Love
43k • written 18 months ago by
samuelcjx
• 0
5
votes
7
replies
1.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 18 months ago by
Gordon Smyth
52k • written 18 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
993
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq
normalization
PCR_efficiency
bias
intrasample_comparison
updated 19 months ago by
James W. MacDonald
67k • written 19 months ago by
FedeXandeR
• 0
0
votes
3
replies
1.1k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq
sequencer
library_size
sequency_depth
multiplexing
offtopic
updated 19 months ago by
James W. MacDonald
67k • written 19 months ago by
FedeXandeR
• 0
1
vote
1
reply
2.3k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 20 months ago by
ATpoint
★ 4.6k • written 20 months ago by
SH
▴ 10
0
votes
1
reply
1.0k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq
Read10X_h5
atac
modalities
updated 20 months ago by
James W. MacDonald
67k • written 20 months ago by
Cynthia
• 0
2
votes
2
replies
1.0k
views
Multifactorial Design for DESEQ2
DESeq2
rna-seq
updated 20 months ago by
ATpoint
★ 4.6k • written 20 months ago by
genome_nerd
• 0
0
votes
1
reply
869
views
Job:
Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell
Spatial
RNA-seq
22 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
990
views
Error in DESeqDataSetFromHTSeqCount
DESeq2
RNA-seq
HTseq
DESeqDataSetFromHTSeqCount
updated 2.0 years ago by
Michael Love
43k • written 2.1 years ago by
abhay.kanodia
• 0
5
votes
9
replies
2.3k
views
GSVA perfomed on RSEM Expected Count data
GSVA
RNA-Seq
RSEM
Expected_Count
2.4 years ago
Yang Shi
▴ 10
2
votes
2
replies
1.5k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma
Clustering
voom
RNA-Seq
2.4 years ago
Yang Shi
▴ 10
0
votes
0
replies
1.1k
views
Job:
Computational Biology Contractor - Chinook Therapeutics
Patient_stratification
Multi-omics
RNA-seq
Kidney_Disease
2.4 years ago
eolson
• 0
2
votes
2
replies
1.2k
views
How to deal with stronger effect by donor than treatment
MDS
RNA-Seq
updated 2.4 years ago by
Gordon Smyth
52k • written 2.4 years ago by
Pei
• 0
0
votes
2
replies
3.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in
RNASeqR
DESeq2
Normalization
rna-seq
updated 15 months ago by
manuel.fernandez
• 0 • written 2.7 years ago by
cicely.day
• 0
3
votes
3
replies
4.0k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER
RNA-seq
differential expression
hidden confounders
updated 2.7 years ago by
ahadli.farid
▴ 30 • written 5.9 years ago by
rodrigo.duarte88
▴ 40
5
votes
5
replies
2.1k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq
PCA
control
DESeq2
Quality
2.8 years ago • updated 2.6 years ago
9906201a
▴ 20
1
vote
5
replies
2.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.8 years ago
Lucy
▴ 60
1
vote
3
replies
1.7k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
samuelcjx
• 0
0
votes
5
replies
4.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq
FPKM
removeBatchEffect
RNA-seq
sva
updated 2.9 years ago by
ATpoint
★ 4.6k • written 3.7 years ago by
Xiaojie Cheng
• 0
0
votes
1
reply
1.1k
views
First time Statistical Analysis of RNA-seq
edgeR
RNA-Seq
log2
foldchange
q_value
updated 2.9 years ago by
Gordon Smyth
52k • written 2.9 years ago by
johndavidgriner74
• 0
1
vote
1
reply
3.3k
views
create S-plots with ropls package
s-plot
ropls
opls-da
rna-seq
updated 3.3 years ago by
Nathalie
▴ 10 • written 4.5 years ago by
andreia
▴ 10
0
votes
5
replies
1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq
DRIMSeq
DEXSeq
rnaseqDTU
3.3 years ago
bioinformatic_trainee
▴ 10
0
votes
0
replies
1.1k
views
Job:
Senior Bioinformatician - University of Alabama at Birmingham
JobPosting
Transcriptomics
SingleCell
RNA-seq
3.4 years ago
lianov
• 0
0
votes
1
reply
1.2k
views
Interaction using a single factor model DESeq2
synergy
DESeq2
RNA-seq
contrast
3.4 years ago • updated 3.3 years ago
slcno
• 0
3
votes
5
replies
3.3k
views
Negative binomial fitting DESeq2
DESeq2
RNA-seq
updated 3.5 years ago by
Michael Love
43k • written 3.5 years ago by
Lucy
▴ 60
0
votes
1
reply
2.3k
views
Doing differential expression using FPKM , samples don't have replication
dge
fpkm
rna-seq
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
lkianmehr
• 0
2
votes
3
replies
1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 3.5 years ago by
Gordon Smyth
52k • written 3.5 years ago by
Alex
• 0
1
vote
1
reply
2.0k
views
Correlation analyses on TCGA data
RNA-seq
Normalization
edgeR
recount3
updated 3.5 years ago by
Leonardo Collado Torres
★ 1.1k • written 3.5 years ago by
mario.keller.1988
▴ 20
3
votes
4
replies
1.3k
views
need help regarding differential expression analysis
rna-seq
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.6 years ago by
Rishav
▴ 20
0
votes
0
replies
1.1k
views
Job:
Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq
Job
Single-Cell
3.6 years ago
rbrns
• 0
1
vote
4
replies
4.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq
recount
updated 3.6 years ago by
Leonardo Collado Torres
★ 1.1k • written 7.2 years ago by
maleknias
• 0
3
votes
4
replies
1.7k
views
Pipeline for an Anova-like analysis in edgeR
edgeR
anova
rna-seq
3.6 years ago
Antonio M.
• 0
1
vote
2
replies
1.3k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 3.7 years ago by
Gordon Smyth
52k • written 3.7 years ago by
athief
▴ 20
1
vote
7
replies
1.7k
views
how to make a contrast of uniquely DE genes
edgeR
limma
RNA-seq
DEGseq
3.7 years ago
decppced
• 0
50 results • Page
1 of 1
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Comment: Cannot install GO.db and org.Hs.eg.db
by
Gabriel
• 0
The downloaded source packages are in 'C:Users\gabri\AppData\Local\Temp\RtmpailNer\downloaded_packages' Installation paths not writeable, …
Comment: Feature Counts - potential bug with outfile.jcounts
by
chris2.a.white
• 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
by
Michael Love
43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts
by
Gordon Smyth
52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag
by
Gordon Smyth
52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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