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2
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5
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1.3k
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Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 9 weeks ago by
Michael Love
41k • written 16 months ago by
kiqbal
• 0
2
votes
5
replies
11k
views
Conversion from counts to FPKM
counts
fpkm
fpkm()
normalization
deseq2
updated 6 months ago by
Hamza
• 0 • written 5.4 years ago by
chiara.facciotto
• 0
3
votes
1
reply
1.4k
views
log2 of normalized counts for further analyzes
DESeq2
log2
normalized
counts
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Laia
▴ 10
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
1
vote
5
replies
8.2k
views
is it possible to use TPM in DESeq2 ?
counts
Normalization
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
0
votes
3
replies
970
views
dealing with outliers (deseq2)
maxcooks
outliers
zero
counts
DESeq2
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
andreia
▴ 10
0
votes
1
reply
920
views
small RNA counts
counts
SmallRNA
Normalization
updated 2.4 years ago by
hauken_heyken
▴ 80 • written 2.5 years ago by
k___
▴ 30
4
votes
4
replies
4.9k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
2
votes
3
replies
2.3k
views
Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind
chipseq
counts
peaks
bedtools
updated 3.0 years ago by
Rory Stark
★ 5.2k • written 6.0 years ago by
Ni-Ar
▴ 10
0
votes
2
replies
3.1k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq
counts
tpm
GenomicFeatures
kallisto
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
m93
• 0
1
vote
8
replies
1.9k
views
[Outlier Gene removal] - One sample with outlier counts for some genes
RNAseq
DESeq2
outlier
counts
DE analysis
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
DcL-A
• 0
2
votes
4
replies
4.6k
views
tximport, Kallisto and Deseq2 (quick answer)
kallisto
tximport
deseq2
counts
5.0 years ago • updated 4.1 years ago
Mozart
▴ 30
0
votes
0
replies
697
views
using gene expression matrix for TCseq package to cluster genes
TCseq
microwarray
cluster
counts
normalization
4.7 years ago
bioyas
▴ 10
5
votes
3
replies
1.3k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger
normalization
counts
RNA-seq
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Tima Karginov
• 0
2
votes
1
reply
1.3k
views
Using DiffBind with only a counts table?
diffbind
ATACseq
ATAC
counts
differential analysis
updated 5.1 years ago by
Rory Stark
★ 5.2k • written 5.1 years ago by
pgontarz
▴ 10
0
votes
7
replies
1.4k
views
Results table completely wrong for specified contrast of
DESeq2
logfoldchange
counts
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
A
▴ 40
0
votes
7
replies
2.3k
views
Count filter for differential expression
edger
limma
counts
updated 5.4 years ago by
Gordon Smyth
50k • written 5.4 years ago by
kaur
• 0
2
votes
4
replies
1.9k
views
why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
deseq2
edger
fpkm
counts
fc
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
ZihaoXing
• 0
1
vote
2
replies
1.2k
views
how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?
deseq2
edger
fpkm
counts
TCGA
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
ZihaoXing
• 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
1
vote
1
reply
953
views
How to compare RNA-seq counts matrices from different aligners ?
rnaseq
counts
alignement
6.1 years ago
Aurora
▴ 20
2
votes
3
replies
3.7k
views
Deseq2: padj value changes with varying alpha
deseq2
counts
rnaseq
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
yoursbassanio
▴ 10
0
votes
5
replies
6.4k
views
unable to find an inherited method for function counts for signature DESeqTransform
deseq2
counts
DESeqtransform
variance
deviation
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
Casper van Mourik
• 0
0
votes
3
replies
1.5k
views
DESeq2 ComputeSumFactors extract normalized counts
deseq2
normalization
counts
updated 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
herrmannmaria94
• 0
0
votes
0
replies
900
views
Combined strand specific and unstranded samples
strand
rnaseq
differential gene expression
batch effect
counts
6.6 years ago
lirongrossmann
▴ 80
4
votes
2
replies
1.8k
views
Help: extract counts from RNA-seq .bam/.bai files
counts
edger
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
mat149
▴ 70
6
votes
4
replies
3.2k
views
Can edgeR TMM normalization be used for other count data?
edgeR
tmm
normalization
counts
updated 7.0 years ago by
James W. MacDonald
65k • written 7.0 years ago by
jol.espinoz
▴ 40
0
votes
1
reply
1.5k
views
IRanges object from count matrix
genomicranges
iranges
featurecounts
counts
rnaseq
updated 7.2 years ago by
Hervé Pagès
16k • written 7.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.2k
views
small RNAs quantification
smallrna
counts
7.6 years ago
ribioinfo
▴ 100
2
votes
1
reply
3.9k
views
DESeq2 Input format
deseq2
counts
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
uzer
• 0
1
vote
3
replies
1.4k
views
DESeq2: Do basemean values take into account interaction effects?
deseq2
counts
normalized counts
updated 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
snamjoshi87
▴ 40
1
vote
4
replies
1.3k
views
comparing transcripts expression between conditions
salmon
transcripts
significance
counts
7.8 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
1.9k
views
Can I calculate counts from the base mean and log2fc outputs of DESeq2? Also, can I calculate error for counts values from lfcse output?
deseq2
chipseq
counts
log2fc
error
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
robin.uchiyama
• 0
3
votes
1
reply
1.4k
views
window counts in csaw
csaw
counts
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
nobishvarghese
• 0
6
votes
12
replies
17k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
wannes.nauwynck
▴ 10
4
votes
3
replies
9.4k
views
How do I extract read counts from DESeq2
deseq2
counts
covariates
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
hechtp
▴ 10
1
vote
3
replies
3.3k
views
HTSeq-count on several gff3/gtf files for use in DESeq2
htseqtools
deseq2
counts
cuffdiff
8.2 years ago
Jon Bråte
▴ 250
2
votes
4
replies
2.5k
views
chromosome name in summarizeOverlaps for RNASeq data
summarizeoverlaps
RNAseq
annotation
counts
8.3 years ago
bioprog
• 0
2
votes
5
replies
3.0k
views
Limma/DESeq2: Statistic and readcount of biological replicates
normalization
limma
deseq2
counts
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
Radek
▴ 90
1
vote
5
replies
1.8k
views
deseq2 normalized data
regression
deseq2
counts
updated 8.6 years ago by
Michael Love
41k • written 8.6 years ago by
akp
• 0
1
vote
1
reply
5.7k
views
Not full rank design using Deseq2
deseq2
design
counts
updated 9.2 years ago by
Michael Love
41k • written 9.2 years ago by
Rainy Gorilla
▴ 30
0
votes
1
reply
1.4k
views
DEXSeq error: Count files do not correspond to the flattened annotation file
DEXSeq
counts
gff
9.5 years ago
Assa Yeroslaviz
★ 1.5k
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma
rnaseq
geneexpression
voom
counts
updated 9.5 years ago by
Steve Lianoglou
★ 13k • written 9.5 years ago by
Peter Crisp
▴ 10
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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