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
3.1k
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
3.9k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 5.5 years ago by
Peter Langfelder
★ 3.0k • written 5.5 years ago by
maya.kappil
▴ 30
9
votes
4
replies
3.4k
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
42k • written 7.2 years ago by
dmr210
▴ 30
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 4 weeks 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
6.3 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
5.4k
views
Trouble with Tximport
tximport
salmon
updated 8.1 years ago by
Michael Love
42k • written 8.1 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
42k • written 6.2 years ago by
pvd2107
▴ 30
4
votes
10
replies
2.9k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 5.3 years ago by
Michael Love
42k • 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 2.4 years ago by
Ming Wang
• 0 • written 6.9 years ago by
macmanes
• 0
4
votes
1
reply
1.1k
views
Adding custom transcript to Salmon index
salmon
updated 21 months ago by
ATpoint
★ 4.1k • written 21 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
4.1 years ago
Michael Love
42k
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
42k • 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 13 months ago by
Michael Love
42k • written 13 months ago by
urwah
▴ 10
3
votes
3
replies
2.5k
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
42k • written 6.9 years ago by
kofoed
• 0
2
votes
6
replies
4.6k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
2.9 years ago
reganhayward
• 0
2
votes
7
replies
2.7k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon
hg38
tximport
tx2gene.csv
updated 7.2 years ago by
Michael Love
42k • 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
42k • 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 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
maya.kappil
▴ 30
2
votes
6
replies
2.0k
views
Normalisation for count data visualisation only
deseq2
salmon
tximport
normalization
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
Alex So
• 0
2
votes
3
replies
937
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport
Salmon
sparse
updated 4.0 years ago by
Michael Love
42k • written 4.0 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
42k • written 5.1 years ago by
saddamhusain77
• 0
2
votes
1
reply
710
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
2.1k
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
2.7 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 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 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
66k • 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 4.7 years ago by
Michael Love
42k • written 4.7 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 5.9 years ago by
Michael Love
42k • written 5.9 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 12 weeks ago by
Michael Love
42k • written 17 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
42k • written 3.0 years ago by
Mikołaj
• 0
2
votes
11
replies
3.1k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
4.5 years ago
mico
• 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
3.9 years ago
keremwai
• 0
1
vote
3
replies
879
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 6.7 years ago by
Michael Love
42k • written 6.7 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
2.2k
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 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
VSM
▴ 120
1
vote
4
replies
2.1k
views
tximport error reading salmon quantification files...
tximport
salmon
updated 7.2 years ago by
James W. MacDonald
66k • written 7.2 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
66k • written 6.0 years ago by
mad6kj
• 0
1
vote
2
replies
2.9k
views
TPM to raw counts
salmon
DESeq2
updated 5 months ago by
bella.johnson.2022
• 0 • written 2.4 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 2.3 years ago by
Michael Love
42k • written 2.3 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
5.6 years ago
fcuy047
• 0
1
vote
5
replies
2.7k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq
salmon
tximport
limma
updated 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 years ago by
Endre Sebestyén
▴ 70
1
vote
2
replies
1.6k
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
1.6k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 4.0 years ago by
Michael Love
42k • written 4.0 years ago by
josephbrown
▴ 10
1
vote
1
reply
898
views
DEseq2 with different fastq read numbers after salmon
deseq2
salmon rna seq
salmon
updated 5.5 years ago by
Michael Love
42k • written 5.5 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 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
kballa
• 0
1
vote
1
reply
1.4k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 5.1 years ago by
Michael Love
42k • written 5.4 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
42k • written 5.2 years ago by
filippo.martignano
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Awards
• All
Popular Question
to
bas_work
▴ 30
Popular Question
to
landenshanie
▴ 40
Popular Question
to
minardsmitha
▴ 10
Teacher
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Mike
• -60
Locations
• All
Netherlands,
just now
France/Marseille/Inserm,
7 minutes ago
Greece,
11 minutes ago
Germany,
14 minutes ago
Spain,
43 minutes ago
Traffic: 698 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