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Showing :
salmon
•
reset
16
votes
25
replies
3.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.9 years ago by
fiona.dick91
▴ 60
12
votes
4
replies
4.6k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 6.2 years ago by
Peter Langfelder
★ 3.0k • written 6.2 years ago by
maya.kappil
▴ 30
9
votes
4
replies
3.9k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
dmr210
▴ 30
6
votes
10
replies
2.9k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 9 months ago by
i.atanasoai
• 0 • written 2.0 years ago by
mohammedtoufiq91
▴ 10
6
votes
10
replies
2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 9 weeks ago by
ATpoint
★ 4.6k • written 10 weeks ago by
mohammedtoufiq91
▴ 10
5
votes
10
replies
13k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love
Salmon
tximport
tx2gene
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
pvd2107
▴ 30
5
votes
9
replies
3.9k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
7.0 years ago
emmak
▴ 20
5
votes
5
replies
5.7k
views
tximport transcript missing
deseq2
salmon
tximport
5.6 years ago
mr6518849
▴ 10
5
votes
9
replies
6.0k
views
Trouble with Tximport
tximport
salmon
updated 8.8 years ago by
Michael Love
43k • written 8.8 years ago by
smithng1215
▴ 30
4
votes
1
reply
1.6k
views
Adding custom transcript to Salmon index
salmon
updated 2.5 years ago by
ATpoint
★ 4.6k • written 2.5 years ago by
Ray
▴ 20
4
votes
5
replies
736
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
3 months ago
LuciaNhu
• 0
4
votes
3
replies
3.8k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport
salmon
R
bioconductor
updated 3.1 years ago by
Ming Wang
• 0 • written 7.6 years ago by
macmanes
• 0
4
votes
0
replies
2.5k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
4.8 years ago
Michael Love
43k
4
votes
10
replies
3.9k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
lkianmehr
• 0
3
votes
4
replies
2.1k
views
quant.sf files and tximport, transcripts not recognized
salmon
tximport
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
Merlin
▴ 10
3
votes
12
replies
2.2k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 22 months ago by
Michael Love
43k • written 22 months ago by
urwah
▴ 10
3
votes
3
replies
2.8k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth
R
salmon rna seq
salmon
7.3 years ago
Walter F. Baumann
▴ 10
2
votes
3
replies
2.9k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq
deseq2
tximport
salmon
normalization
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
kofoed
• 0
2
votes
3
replies
2.2k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
maya.kappil
▴ 30
2
votes
7
replies
3.0k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon
hg38
tximport
tx2gene.csv
updated 7.9 years ago by
Michael Love
43k • written 7.9 years ago by
seb.boegel
• 0
2
votes
6
replies
2.3k
views
Normalisation for count data visualisation only
deseq2
salmon
tximport
normalization
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
Alex So
• 0
2
votes
8
replies
2.2k
views
Transcript variant analysis on Salmon output
Salmon
RNA-Seq
Transcript variant analysis
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
saddamhusain77
• 0
2
votes
7
replies
2.4k
views
RNA-seq with Salmon and tximport
RNA-seq
Salmon
tximport
updated 5.5 years ago by
James W. MacDonald
68k • written 5.5 years ago by
woojoy14
• 0
2
votes
3
replies
1.6k
views
Using duplication rate as a covariate
deseq2
salmon
fastp
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
rbutler
• 0
2
votes
3
replies
2.1k
views
scater/scran with TPMs from Salmon - counts?
scater
salmon
scran
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
nk
▴ 10
2
votes
11
replies
3.6k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
5.3 years ago • updated 5.2 years ago
mico
• 0
2
votes
1
reply
1.8k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport
salmon
deseq2
updated 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
AKSR
▴ 20
2
votes
2
replies
1.4k
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
4.6 years ago
keremwai
• 0
2
votes
3
replies
1.2k
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport
Salmon
sparse
updated 4.7 years ago by
Michael Love
43k • written 4.7 years ago by
noorpratap
• 0
2
votes
6
replies
5.5k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
3.7 years ago • updated 3.6 years ago
reganhayward
• 0
2
votes
1
reply
1.2k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq
Salmon
DESeq2
updated 3.7 years ago by
Michael Love
43k • written 3.8 years ago by
Mikołaj
• 0
2
votes
5
replies
2.1k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 11 months ago by
Michael Love
43k • written 2.1 years ago by
kiqbal
• 0
2
votes
2
replies
2.8k
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
3.4 years ago
Qin
▴ 10
2
votes
9
replies
1.5k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon
edger
tximport
rnaseq
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
martin.weihrauch
▴ 20
2
votes
7
replies
1.9k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq
salmon
alpine
transcript expression
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
relathman
▴ 20
2
votes
1
reply
1.0k
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 2.1 years ago by
ATpoint
★ 4.6k • written 2.1 years ago by
Dunois
• 0
1
vote
1
reply
1.6k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 5.8 years ago by
Michael Love
43k • written 6.1 years ago by
fiona.dick91
▴ 60
1
vote
4
replies
1.6k
views
comparing transcripts expression between conditions
salmon
transcripts
significance
counts
8.6 years ago
Assa Yeroslaviz
★ 1.5k
1
vote
5
replies
2.1k
views
How to filter tximport output for edgeR?
tximport
edger
salmon
rna-seq
updated 8.3 years ago by
Michael Love
43k • written 8.3 years ago by
Peter
• 0
1
vote
4
replies
2.4k
views
tximport error reading salmon quantification files...
tximport
salmon
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
nschurch
▴ 20
1
vote
5
replies
3.2k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq
salmon
tximport
limma
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
Endre Sebestyén
▴ 70
1
vote
5
replies
3.6k
views
tximport using for data generated from other tools
tximport
salmon
eXpress
updated 6.8 years ago by
Michael Love
43k • written 7.7 years ago by
saumya.kumar
• 0
1
vote
0
replies
2.2k
views
How to test or estimate differential TSS/promoter usage/expression based on RNA-seq data only
tximport
differential isoform usage
salmon
tss
rna-seq
7.6 years ago
Steffen Heyne
▴ 10
1
vote
5
replies
2.3k
views
tximport error with salmon version
deseq2
salmon
tximport
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
agetzler
• 0
1
vote
4
replies
1.7k
views
Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
salmon
tximport
limma-voom
updated 7.4 years ago by
Michael Love
43k • written 7.4 years ago by
Sandip Darji
▴ 30
1
vote
4
replies
2.5k
views
processing of (salmon) gene counts for eqtl analysis
salmon
tximport
gene length
eqtl
TMM
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
VSM
▴ 120
1
vote
1
reply
1.4k
views
Controlling for batch after Salmon-Tximport
deseq2
wgcna
salmon
rna-seq
DESeq2
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
mad6kj
• 0
1
vote
2
replies
1.3k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
6.3 years ago
fcuy047
• 0
1
vote
1
reply
1.1k
views
DEseq2 with different fastq read numbers after salmon
deseq2
salmon rna seq
salmon
updated 6.2 years ago by
Michael Love
43k • written 6.2 years ago by
danalvoronov
▴ 10
1
vote
3
replies
1.9k
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon
deseq2
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
kballa
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: GSVA on RNAseq data
by
Robert Castelo
★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell
by
James W. MacDonald
68k
Put it in a list and put the list in a column.
Comment: For some reason I can't update BiocManager to 3.20
by
James W. MacDonald
68k
Please post output from starting R and then running `sessionInfo()` (as requested by the web form you use to post questions). I get ``` > …
Comment: p-value the same for different contrasts DESeq2
by
caroline.zanchi
• 0
It would be great if it were possible to do something similar using GlmGamPoi !
Comment: Web accessibility of Bioconductor.org
by
Sean Davis
21k
Added issue to website github repo: https://github.com/Bioconductor/bioconductor.org/issues/304
Votes
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
Answer: Standardization of rlog transformed counts before PCA
A: Rtracklayer fails to export TxDb as GFF3 without CDS
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