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Showing :
Salmon
•
reset
0
votes
1
reply
45
views
Adding custom transcript to Salmon index
salmon
updated 2 days ago by
ATpoint
★ 1.4k • written 2 days ago by
Ray
• 0
1
vote
3
replies
373
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 6 months ago by
Michael Love
37k • written 6 months ago by
samuelcjx
• 0
0
votes
1
reply
205
views
tximport
salmon
tximport
updated 6 months ago by
Michael Love
37k • written 6 months ago by
Pragathi
• 0
1
vote
1
reply
222
views
TPM to raw counts
salmon
DESeq2
updated 7 months ago by
Steve Lianoglou
13k • written 7 months ago by
Sneha
• 0
0
votes
4
replies
577
views
Filtering output from tximport
tximport
Salmon
updated 9 months ago by
Michael Love
37k • written 9 months ago by
Sheean
• 0
2
votes
2
replies
553
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
11 months ago • updated 10 months ago
Qin
▴ 10
0
votes
2
replies
475
views
Error message when importing my quant.sf files into R using tximport; should I set 'ignoreTxVersion' to True or False?
Salmon
ignoreTxVersion
tximport
updated 11 months ago by
Michael Love
37k • written 11 months ago by
robeaumont
• 0
0
votes
14
replies
1.0k
views
Best practice for quantifying sncRNA
Salmon
sncRNA
RNASeq
12 months ago
Abhishek
• 0
2
votes
6
replies
1.4k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
14 months ago
reganhayward
• 0
2
votes
1
reply
399
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq
Salmon
DESeq2
updated 15 months ago by
Michael Love
37k • written 15 months ago by
Mikołaj
• 0
1
vote
2
replies
724
views
Regarding transcripts to gene ID conversion in tximport
salmon
tximport
DESeq2
17 months ago
Nikolay Ivanov
• 0
0
votes
7
replies
782
views
Subtracting Background Signal Before DESeq Analysis
Salmon
DESeq2
updated 14 months ago by
Michael Love
37k • written 18 months ago by
vanbelj
▴ 10
0
votes
2
replies
391
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon
EnsDb.Hsapiens.v86
tximport
updated 18 months ago by
James W. MacDonald
60k • written 18 months ago by
TJ
• 0
0
votes
5
replies
678
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 2.0 years ago by
Michael Love
37k • written 2.0 years ago by
Charlotte
• 0
2
votes
1
reply
543
views
tximport samples.txt file mandatory vs. optional colnames?
tximport
salmon
deseq2
updated 2.0 years ago by
Michael Love
37k • written 2.0 years ago by
AKSR
▴ 20
2
votes
2
replies
472
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
2.1 years ago
keremwai
• 0
2
votes
3
replies
362
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport
Salmon
sparse
updated 2.2 years ago by
Michael Love
37k • written 2.2 years ago by
noorpratap
• 0
0
votes
3
replies
450
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2
edgeR
salmon
tximport
updated 2.2 years ago by
Michael Love
37k • written 2.2 years ago by
iaradsouza1
• 0
1
vote
3
replies
663
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 2.3 years ago by
Michael Love
37k • written 2.3 years ago by
josephbrown
▴ 10
0
votes
4
replies
395
views
Having a hard time creating a Txi object from an existing Salmon output file to convert transcript file to gene id TPM
Salmon
tximport
tximportdata
ensembl
updated 2.3 years ago by
Michael Love
37k • written 2.3 years ago by
slouis
• 0
4
votes
0
replies
1.1k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
2.3 years ago
Michael Love
37k
0
votes
6
replies
453
views
tximport lose transcript names with Salmon bootstrap
salmon
tximport
bootstrap
updated 2.4 years ago by
julia.jefferson23
• 0 • written 2.4 years ago by
Cindy
• 0
0
votes
3
replies
1.1k
views
"lexical error: invalid char in json text" when using tximport
tximport
salmon
updated 2.5 years ago by
Michael Love
37k • written 2.5 years ago by
alallo
• 0
0
votes
1
reply
555
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2
tximport
salmon
updated 2.5 years ago by
Michael Love
37k • written 2.5 years ago by
gmchaput
• 0
0
votes
5
replies
646
views
Changing Gene ID annotation style - working with Salmon output [NM...] and resulting count files are numeric-only IDs
tximport
Gene IDs
txdb
RefSeq
Salmon
updated 2.6 years ago by
Michael Love
37k • written 2.6 years ago by
holmkn
• 0
0
votes
5
replies
487
views
importing salmon rnaseq quant with tximeta
tximeta
salmon
deseq2
2.6 years ago
omid.alamdari
• 0
2
votes
11
replies
1.7k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
2.8 years ago • updated 2.7 years ago
mico
• 0
1
vote
3
replies
371
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon
DESeq2
updated 2.8 years ago by
Kevin Blighe
3.6k • written 2.8 years ago by
guanwang179
▴ 10
0
votes
8
replies
1.2k
views
IgnoreTxVersion on Tximport not working
Tximport
Salmon
2.9 years ago
k1mukund
• 0
1
vote
2
replies
422
views
Normalizing counts using TIN metric before DESeq2
deseq2
tximport
salmon
updated 2.9 years ago by
Michael Love
37k • written 2.9 years ago by
hsbio
▴ 10
2
votes
3
replies
543
views
Using duplication rate as a covariate
deseq2
salmon
fastp
updated 2.9 years ago by
Michael Love
37k • written 2.9 years ago by
rbutler
• 0
2
votes
7
replies
1.1k
views
RNA-seq with Salmon and tximport
RNA-seq
Salmon
tximport
updated 3.0 years ago by
James W. MacDonald
60k • written 3.0 years ago by
woojoy14
• 0
1
vote
1
reply
503
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR
Salmon
3.0 years ago
konstantinos.bogias
▴ 10
5
votes
5
replies
2.8k
views
tximport transcript missing
deseq2
salmon
tximport
3.1 years ago
mr6518849
▴ 10
0
votes
2
replies
438
views
Importing Salmon counts with tximport with host and virus genomes
salmon
tximport
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
rbenel
▴ 20
1
vote
3
replies
498
views
DESeq2 gives weird results
deseq2
salmon
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
chipolino
• 0
1
vote
1
reply
812
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 3.3 years ago by
Michael Love
37k • written 3.6 years ago by
fiona.dick91
▴ 10
1
vote
9
replies
1.3k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR
tximport
rnaseq
salmon
updated 3.4 years ago by
k.vitting.seerup
▴ 120 • written 3.4 years ago by
saddamhusain77
• 0
1
vote
5
replies
1.3k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
updated 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
fiona.dick91
▴ 10
2
votes
8
replies
714
views
Transcript variant analysis on Salmon output
Salmon
RNA-Seq
Transcript variant analysis
updated 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
saddamhusain77
• 0
3
votes
4
replies
730
views
quant.sf files and tximport, transcripts not recognized
salmon
tximport
updated 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
Merlin
▴ 10
1
vote
1
reply
550
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
filippo.martignano
• 0
1
vote
6
replies
1.3k
views
Normalisation for count data visualisation only
deseq2
salmon
tximport
normalization
updated 3.4 years ago by
Michael Love
37k • written 3.4 years ago by
Alex So
• 0
4
votes
10
replies
1.1k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 3.6 years ago by
Michael Love
37k • written 3.6 years ago by
lkianmehr
• 0
1
vote
3
replies
965
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon
deseq2
updated 3.6 years ago by
Michael Love
37k • written 3.6 years ago by
kballa
• 0
8
votes
4
replies
2.1k
views
WGCNA following salmon/DESeq2
deseq2
wgcna
salmon
updated 3.7 years ago by
Peter Langfelder
★ 2.7k • written 3.7 years ago by
maya.kappil
▴ 20
2
votes
3
replies
961
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon
edaseq
rna-seq
deseq2
updated 3.7 years ago by
Michael Love
37k • written 3.7 years ago by
maya.kappil
▴ 20
1
vote
1
reply
479
views
DEseq2 with different fastq read numbers after salmon
deseq2
salmon rna seq
salmon
updated 3.7 years ago by
Michael Love
37k • written 3.7 years ago by
danalvoronov
▴ 10
0
votes
0
replies
555
views
quantifying piRNA and tRNA by Salmon
Salmon
DGE
3.8 years ago
lkianmehr
• 0
1
vote
2
replies
598
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport
tximportdata
salmon
3.8 years ago
fcuy047
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: mapToAlignments_issue
by
Hervé Pagès
15k
> I would expect in case of reverse alignment lifted ranges to correspond to position 91-100 of the query sequence. Nope. Local coordinate…
Answer: Problem related to `biomaRt::getBM()` during `R CMD check` execution
by
James W. MacDonald
60k
Does the section in the biomaRt vignette that talks about caching (and using a temp dir) help?
Comment: OPLS-DA: confidence interval for accuracy metric
by
Eddie
• 0
Worked well under pROC. Thank you
Comment: errors in annotation
by
James W. MacDonald
60k
If you go to NCBI and the data appear to be correct, then they have evidently already fixed the errors you have found. The data we download…
Comment: How should I set my eps value in cluster profiler?
by
Guido Hooiveld
★ 3.3k
Under the hood `clusterProfiler` makes use of a (fast) GSEA algorithm implemented in the package `fgsea` (function `fgseaMultilevel`). The …
Votes
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
How to select summit size for histone ChiP-Seq in Diffbind
Comment: GSEA with Wikipathways not entirely reproducible
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