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salmon
•
reset
0
votes
4
replies
1.7k
views
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2
salmon
tximport
7.5 years ago
bruno.saubamea
• 0
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
★ 4.7k • written 11 weeks ago by
mohammedtoufiq91
▴ 10
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
0
votes
2
replies
1.3k
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 2.1 years ago by
camilia.savitri
• 0
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
0
votes
6
replies
3.2k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport
DESeq2
"tximport"
deseq2
salmon
7.7 years ago
sunil.mangalam
• 0
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
0
votes
2
replies
1.2k
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon
EnsDb.Hsapiens.v86
tximport
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
TJ
• 0
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
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
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
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
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
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
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
0
votes
2
replies
2.8k
views
use tximport's countsFromAbundance when using DESeq2
deseq2
tximport
normalization
salmon
rnaseq
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
ginlucks
• 0
0
votes
1
reply
1.0k
views
tximport error with Salmon in DESeq2 pipeline
tximport
deseq2
salmon
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
seyfim
• 0
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
0
votes
6
replies
1.4k
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2
salmon
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
andrewpountain
• 0
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
0
votes
3
replies
4.9k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb
tximport
salmon
updated 6.7 years ago by
Johannes Rainer
★ 2.1k • written 6.7 years ago by
user31888
▴ 30
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
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
2
votes
3
replies
2.3k
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
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
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
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
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
1
vote
1
reply
1.3k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
filippo.martignano
• 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
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
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
1
vote
9
replies
3.0k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR
tximport
rnaseq
salmon
updated 5.9 years ago by
k.vitting.seerup
▴ 120 • written 5.9 years ago by
saddamhusain77
• 0
1
vote
3
replies
1.4k
views
DESeq2 gives weird results
deseq2
salmon
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
chipolino
• 0
0
votes
2
replies
1.2k
views
Importing Salmon counts with tximport with host and virus genomes
salmon
tximport
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
rbenel
▴ 40
5
votes
5
replies
5.7k
views
tximport transcript missing
deseq2
salmon
tximport
5.6 years ago
mr6518849
▴ 10
4
votes
5
replies
740
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
3 months ago
LuciaNhu
• 0
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
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
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
2
votes
7
replies
3.1k
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
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
0
votes
1
reply
1.4k
views
salmon quantification - identical transcripts in fasta file
salmon
updated 7.9 years ago by
James W. MacDonald
68k • written 7.9 years ago by
dmr210
▴ 30
1
vote
2
replies
2.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon
IsoformSwitchAnalyzeR
tximport
RNASeqData
updated 18 months ago by
k.vitting.seerup
▴ 120 • written 18 months ago by
elva.gypsophila
▴ 10
6
votes
10
replies
3.0k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 10 months ago by
i.atanasoai
• 0 • written 2.0 years ago by
mohammedtoufiq91
▴ 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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Overcoming confounding in batch effect correction
by
Dario Strbenac
★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
biostars.org and the [bioinformatics reddit][1] are suitable and have much larger audience than this forum here. [1]: https://www.reddi…
Comment: Overcoming confounding in batch effect correction
by
bbao
▴ 10
Thank you! And apologies for posting here. Do you know which forum I should go to in the future for questions like these?
Comment: For some reason I can't update BiocManager to 3.20
by
shepherl
4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction
by
ATpoint
★ 4.7k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Votes
Answer: Store Matrix in DataFrame Cell
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
Comment: Overcoming confounding in batch effect correction
Overcoming confounding in batch effect correction
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