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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 4 months ago by
swbarnes2
★ 1.3k • written 4 months ago by
Bo
• 0
0
votes
1
reply
570
views
Help for RNA sequencing analysis with DESEQ2
DESeq2
star
differentiallyexpressed
updated 15 months ago by
Michael Love
41k • written 15 months ago by
nico
• 0
0
votes
1
reply
1.9k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads
STAR
featureCounts
updated 16 months ago by
swbarnes2
★ 1.3k • written 16 months ago by
lalala
• 0
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
josephbrown
▴ 10
0
votes
1
reply
1.7k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
mohamedrefaat.1.1992
• 0
0
votes
1
reply
887
views
Using STAR and DESeq2 for circRNA analysis
STAR
deseq2
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
csijst
• 0
3
votes
2
replies
2.1k
views
The optimal minMQS parameter in featureCounts for RNA-Seq quantification
RNA-Seq
featureCounts
STAR
minMQS
mapping quality score
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
Gary
▴ 20
0
votes
1
reply
904
views
weired output with featurecount
featurecounts
star
5.6 years ago
roghaiyeh.safari
• 0
0
votes
3
replies
3.3k
views
Handling pseudogenes in RNA-seq
rna-seq
pseudogenes
STAR
counts
updated 5.9 years ago by
Levi Waldron
★ 1.1k • written 5.9 years ago by
supremerulersuraj
• 0
0
votes
2
replies
2.9k
views
lncRNA annotation for featureCouns and STAR
lncRNA
featureCounts
STAR
annotation
updated 5.9 years ago by
Wei Shi
★ 3.6k • written 5.9 years ago by
inah
▴ 10
0
votes
2
replies
1.1k
views
BAM file into R from Illumina
bam file
STAR
Illumina
updated 6.0 years ago by
ta_awwad
▴ 10 • written 6.0 years ago by
soheilazareie
• 0
2
votes
2
replies
1.1k
views
Why does total unique map not equal to library size?
htseqcounts
star
rnaseq
6.6 years ago
Ahdee
▴ 50
2
votes
2
replies
7.3k
views
RNA STAR to DESeq2
deseq2
count matrix
star
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
nikelle.petrillo
• 0
1
vote
2
replies
1.5k
views
Gviz off-by-one with STAR BAM
gviz
off-by-one
STAR
BAM
coverage
updated 7.1 years ago by
Martin Morgan
25k • written 7.1 years ago by
bernt.popp
• 0
1
vote
7
replies
5.3k
views
featureCounts creating fragments and high NoFeatures value
featurecounts
bioconductor
differential gene expression
star
updated 7.2 years ago by
Wei Shi
★ 3.6k • written 7.2 years ago by
gregory.l.stone
▴ 10
0
votes
10
replies
4.7k
views
Differential expression analysis for STAR-aligned RNA-Seq data
deseq2
rnaseq
STAR
updated 7.7 years ago by
Michael Love
41k • written 7.7 years ago by
sum31278
• 0
4
votes
7
replies
2.1k
views
RNAseq reads mapped to the gene
star
featurecounts
edgeR
RNAseq
7.9 years ago
myprogramming2016
• 0
0
votes
0
replies
1.1k
views
STAR_how many mismatches to allow if the read length is 100 bp in RNA-seq data
star
8.4 years ago
tg369
▴ 10
0
votes
5
replies
2.8k
views
Problem Importing STAR fusion data into chimera
fusion genes
chimera
star
updated 9.1 years ago by
richa_r
• 0 • written 9.5 years ago by
am26
• 0
1
vote
5
replies
2.2k
views
Single end STAR Chimeric.out.junction fails to read with chimera::importFusionData
chimera
STAR
updated 9.2 years ago by
rcaloger
▴ 500 • written 9.3 years ago by
wresch
• 0
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Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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