Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Salmon
•
reset
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
12
votes
4
replies
3.8k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 5.4 years ago by
Peter Langfelder
★ 3.0k • written 5.4 years ago by
maya.kappil
▴ 30
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon
cqn
tximport
deseq2
rnaseq
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
dmr210
▴ 30
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 13 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
5
votes
9
replies
3.5k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
6.2 years ago
emmak
▴ 20
5
votes
5
replies
4.9k
views
tximport transcript missing
deseq2
salmon
tximport
4.8 years ago
mr6518849
▴ 10
5
votes
9
replies
5.3k
views
Trouble with Tximport
tximport
salmon
updated 8.0 years ago by
Michael Love
41k • written 8.0 years ago by
smithng1215
▴ 30
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love
Salmon
tximport
tx2gene
updated 6.2 years ago by
Michael Love
41k • written 6.2 years ago by
pvd2107
▴ 30
4
votes
10
replies
2.8k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
lkianmehr
• 0
4
votes
3
replies
3.4k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport
salmon
R
bioconductor
updated 2.3 years ago by
Ming Wang
• 0 • written 6.8 years ago by
macmanes
• 0
4
votes
1
reply
1.1k
views
Adding custom transcript to Salmon index
salmon
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
Ray
▴ 20
4
votes
0
replies
2.1k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
4.0 years ago
Michael Love
41k
3
votes
4
replies
1.7k
views
quant.sf files and tximport, transcripts not recognized
salmon
tximport
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Merlin
▴ 10
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon
RUVSeq
cqn
PCA
RNASeq
updated 12 months ago by
Michael Love
41k • written 12 months ago by
urwah
▴ 10
3
votes
3
replies
2.4k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth
R
salmon rna seq
salmon
6.5 years ago
Walter F. Baumann
▴ 10
2
votes
3
replies
2.5k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq
deseq2
tximport
salmon
normalization
updated 6.9 years ago by
Michael Love
41k • written 6.9 years ago by
kofoed
• 0
2
votes
6
replies
4.5k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.9 years ago
reganhayward
• 0
2
votes
7
replies
2.6k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon
hg38
tximport
tx2gene.csv
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
seb.boegel
• 0
2
votes
1
reply
1.5k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport
salmon
deseq2
updated 3.8 years ago by
Michael Love
41k • written 3.8 years ago by
AKSR
▴ 20
2
votes
3
replies
1.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
maya.kappil
▴ 30
2
votes
6
replies
2.0k
views
Normalisation for count data visualisation only
deseq2
salmon
tximport
normalization
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
Alex So
• 0
2
votes
3
replies
928
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport
Salmon
sparse
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
noorpratap
• 0
2
votes
8
replies
1.6k
views
Transcript variant analysis on Salmon output
Salmon
RNA-Seq
Transcript variant analysis
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
saddamhusain77
• 0
2
votes
1
reply
679
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 16 months ago by
ATpoint
★ 4.1k • written 16 months ago by
Dunois
• 0
2
votes
2
replies
2.0k
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
2.6 years ago
Qin
▴ 10
2
votes
9
replies
1.3k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon
edger
tximport
rnaseq
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
martin.weihrauch
▴ 20
2
votes
7
replies
2.0k
views
RNA-seq with Salmon and tximport
RNA-seq
Salmon
tximport
updated 4.7 years ago by
James W. MacDonald
65k • written 4.7 years ago by
woojoy14
• 0
2
votes
3
replies
1.3k
views
Using duplication rate as a covariate
deseq2
salmon
fastp
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
rbutler
• 0
2
votes
7
replies
1.6k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq
salmon
alpine
transcript expression
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
relathman
▴ 20
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 10 weeks ago by
Michael Love
41k • written 16 months ago by
kiqbal
• 0
2
votes
1
reply
1.0k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq
Salmon
DESeq2
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
Mikołaj
• 0
2
votes
11
replies
3.0k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
4.5 years ago • updated 4.4 years ago
mico
• 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
3.8 years ago
keremwai
• 0
1
vote
3
replies
860
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon
DESeq2
updated 4.5 years ago by
Kevin Blighe
★ 3.9k • written 4.5 years ago by
guanwang179
▴ 10
1
vote
4
replies
1.4k
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 6.6 years ago by
Michael Love
41k • written 6.6 years ago by
Sandip Darji
▴ 30
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater
salmon
scran
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
nk
• 0
1
vote
2
replies
2.1k
views
Regarding transcripts to gene ID conversion in tximport
salmon
tximport
DESeq2
3.2 years ago
Nikolay Ivanov
• 0
1
vote
4
replies
2.1k
views
processing of (salmon) gene counts for eqtl analysis
salmon
tximport
gene length
eqtl
TMM
updated 6.0 years ago by
Michael Love
41k • written 6.0 years ago by
VSM
▴ 120
1
vote
4
replies
2.1k
views
tximport error reading salmon quantification files...
tximport
salmon
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
nschurch
▴ 20
1
vote
1
reply
1.2k
views
Controlling for batch after Salmon-Tximport
deseq2
wgcna
salmon
rna-seq
DESeq2
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
mad6kj
• 0
1
vote
2
replies
2.8k
views
TPM to raw counts
salmon
DESeq2
updated 5 months ago by
bella.johnson.2022
• 0 • written 2.3 years ago by
Sneha
• 0
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
samuelcjx
• 0
1
vote
2
replies
1.0k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
5.5 years ago
fcuy047
• 0
1
vote
5
replies
2.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq
salmon
tximport
limma
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
Endre Sebestyén
▴ 70
1
vote
2
replies
1.5k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 9 months ago by
k.vitting.seerup
▴ 120 • written 9 months ago by
elva.gypsophila
▴ 10
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
1
vote
1
reply
888
views
DEseq2 with different fastq read numbers after salmon
deseq2
salmon rna seq
salmon
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
danalvoronov
▴ 10
1
vote
3
replies
1.6k
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon
deseq2
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
kballa
• 0
1
vote
1
reply
1.4k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 5.0 years ago by
Michael Love
41k • written 5.3 years ago by
fiona.dick91
▴ 60
1
vote
1
reply
1.0k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
filippo.martignano
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards
• All
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Popular Question
to
shepherl
3.9k
Popular Question
to
siajunren
• 0
Scholar
to
Rory Stark
★ 5.2k
Locations
• All
WEHI, Melbourne, Australia,
3 minutes ago
France,
14 minutes ago
St Louis, MO,
2 hours ago
United States,
2 hours ago
United States,
3 hours ago
Traffic: 620 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6