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Showing :
salmon
•
reset
0
votes
2
replies
123
views
how to match salmon output to txname
GenomicFeatures
tximport
salmon
written 28 days ago by
camilia.savitri
• 0
0
votes
1
reply
105
views
Missing transcript
DESeq2
tximport
salmon
updated 4 weeks ago by
ATpoint
★ 2.1k • written 4 weeks ago by
camilia.savitri
• 0
2
votes
1
reply
120
views
Confused about tximport-DESeq2 setup
DESeq2
tximport
salmon
updated 4 weeks ago by
ATpoint
★ 2.1k • written 4 weeks ago by
Dunois
• 0
2
votes
2
replies
159
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
written 6 weeks ago by
kiqbal
• 0
0
votes
1
reply
142
views
Trouble with importing transcript counts with Salmon
Salmon
tximport
RNAseq
EdgeR
updated 11 weeks ago by
ATpoint
★ 2.1k • written 11 weeks ago by
Jenni
• 0
0
votes
2
replies
255
views
dose NumReads obtained with 'salmon -g' provide suitable inputs to DESeq2
DESeq2
salmon
3 months ago
manduchi
▴ 10
0
votes
1
reply
245
views
Adding custom transcript to Salmon index
salmon
updated 5 months ago by
ATpoint
★ 2.1k • written 5 months ago by
Ray
• 0
1
vote
3
replies
604
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon
rna-seq
swish
bootstrap
fishpond
updated 11 months ago by
Michael Love
39k • written 12 months ago by
samuelcjx
• 0
0
votes
1
reply
347
views
tximport
salmon
tximport
updated 12 months ago by
Michael Love
39k • written 12 months ago by
Pragathi
• 0
1
vote
1
reply
821
views
TPM to raw counts
salmon
DESeq2
updated 13 months ago by
Steve Lianoglou
13k • written 13 months ago by
Sneha
• 0
0
votes
4
replies
821
views
Filtering output from tximport
tximport
Salmon
updated 14 months ago by
Michael Love
39k • written 14 months ago by
Sheean
• 0
2
votes
2
replies
866
views
Volcano plots of DEGs from Swish are weird
DESeq2
fishpond
salmon
swish
17 months ago • updated 16 months ago
Qin
▴ 10
0
votes
2
replies
723
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 17 months ago by
Michael Love
39k • written 17 months ago by
robeaumont
• 0
0
votes
14
replies
1.3k
views
Best practice for quantifying sncRNA
Salmon
sncRNA
RNASeq
18 months ago
Abhishek
• 0
2
votes
6
replies
2.4k
views
Salmon, RUVSeq and DESeq2
Salmon
DESeq2
DEG
RUVSeq
20 months ago • updated 19 months ago
reganhayward
• 0
2
votes
1
reply
558
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq
Salmon
DESeq2
updated 20 months ago by
Michael Love
39k • written 21 months ago by
Mikołaj
• 0
1
vote
2
replies
1.0k
views
Regarding transcripts to gene ID conversion in tximport
salmon
tximport
DESeq2
23 months ago
Nikolay Ivanov
• 0
0
votes
7
replies
996
views
Subtracting Background Signal Before DESeq Analysis
Salmon
DESeq2
updated 20 months ago by
Michael Love
39k • written 23 months ago by
vanbelj
▴ 20
0
votes
2
replies
516
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon
EnsDb.Hsapiens.v86
tximport
updated 2.0 years ago by
James W. MacDonald
62k • written 2.0 years ago by
TJ
• 0
0
votes
5
replies
816
views
Error using DRIMSeq with Salmon count data
DRIMSeq
tximport
txdb
Salmon
updated 2.5 years ago by
Michael Love
39k • written 2.5 years ago by
Charlotte
• 0
2
votes
1
reply
794
views
tximport samples.txt file mandatory vs. optional colnames?
tximport
salmon
deseq2
updated 2.5 years ago by
Michael Love
39k • written 2.5 years ago by
AKSR
▴ 20
2
votes
2
replies
592
views
Tximport missing values for group summarizing counts
tximport
rat
reference
GTF
salmon
2.6 years ago
keremwai
• 0
2
votes
3
replies
473
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport
Salmon
sparse
updated 2.7 years ago by
Michael Love
39k • written 2.7 years ago by
noorpratap
• 0
0
votes
3
replies
641
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2
edgeR
salmon
tximport
updated 2.7 years ago by
Michael Love
39k • written 2.7 years ago by
iaradsouza1
• 0
1
vote
3
replies
884
views
tximeta on STAR-aligned Salmon-quantified output
tximeta
salmon
STAR
updated 2.7 years ago by
Michael Love
39k • written 2.7 years ago by
josephbrown
▴ 10
0
votes
4
replies
542
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 2.8 years ago by
Michael Love
39k • written 2.8 years ago by
slouis
• 0
4
votes
0
replies
1.3k
views
Tutorial:
How to post Salmon data to GEO for use with tximeta
salmon
tximeta
Tutorial
2.8 years ago
Michael Love
39k
0
votes
6
replies
559
views
tximport lose transcript names with Salmon bootstrap
salmon
tximport
bootstrap
updated 2.9 years ago by
julia.jefferson23
• 0 • written 2.9 years ago by
Cindy
• 0
0
votes
3
replies
1.5k
views
"lexical error: invalid char in json text" when using tximport
tximport
salmon
updated 3.0 years ago by
Michael Love
39k • written 3.0 years ago by
alallo
• 0
0
votes
1
reply
675
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2
tximport
salmon
updated 3.0 years ago by
Michael Love
39k • written 3.0 years ago by
gmchaput
• 0
0
votes
5
replies
945
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 3.0 years ago by
Michael Love
39k • written 3.0 years ago by
holmkn
• 0
0
votes
5
replies
634
views
importing salmon rnaseq quant with tximeta
tximeta
salmon
deseq2
3.1 years ago
omid.alamdari
• 0
2
votes
11
replies
1.9k
views
Cannot find header.json in salmon index directory
salmon
tximeta
rna-seq
3.2 years ago
mico
• 0
1
vote
3
replies
447
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon
DESeq2
updated 3.3 years ago by
Kevin Blighe
3.7k • written 3.3 years ago by
guanwang179
▴ 10
0
votes
8
replies
1.7k
views
IgnoreTxVersion on Tximport not working
Tximport
Salmon
3.4 years ago
k1m
▴ 10
1
vote
2
replies
512
views
Normalizing counts using TIN metric before DESeq2
deseq2
tximport
salmon
updated 3.4 years ago by
Michael Love
39k • written 3.4 years ago by
hsbio
▴ 10
2
votes
3
replies
703
views
Using duplication rate as a covariate
deseq2
salmon
fastp
updated 3.4 years ago by
Michael Love
39k • written 3.4 years ago by
rbutler
• 0
2
votes
7
replies
1.2k
views
RNA-seq with Salmon and tximport
RNA-seq
Salmon
tximport
updated 3.4 years ago by
James W. MacDonald
62k • written 3.4 years ago by
woojoy14
• 0
1
vote
1
reply
591
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR
Salmon
3.5 years ago
konstantinos.bogias
▴ 10
5
votes
5
replies
3.4k
views
tximport transcript missing
deseq2
salmon
tximport
3.5 years ago
mr6518849
▴ 10
0
votes
2
replies
525
views
Importing Salmon counts with tximport with host and virus genomes
salmon
tximport
updated 3.6 years ago by
Michael Love
39k • written 3.6 years ago by
rbenel
▴ 20
1
vote
3
replies
637
views
DESeq2 gives weird results
deseq2
salmon
updated 3.7 years ago by
Michael Love
39k • written 3.7 years ago by
chipolino
• 0
1
vote
1
reply
905
views
rnaseqDTU log2fold change DEXSeq
DEXSeq
DTU
salmon
rnaseqDTU
foldchange
updated 3.8 years ago by
Michael Love
39k • written 4.1 years ago by
fiona.dick91
▴ 10
1
vote
9
replies
1.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR
tximport
rnaseq
salmon
updated 3.8 years ago by
k.vitting.seerup
▴ 120 • written 3.8 years ago by
saddamhusain77
• 0
1
vote
5
replies
1.6k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
updated 3.8 years ago by
Michael Love
39k • written 3.8 years ago by
fiona.dick91
▴ 10
2
votes
8
replies
869
views
Transcript variant analysis on Salmon output
Salmon
RNA-Seq
Transcript variant analysis
updated 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
saddamhusain77
• 0
3
votes
4
replies
905
views
quant.sf files and tximport, transcripts not recognized
salmon
tximport
updated 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
Merlin
▴ 10
1
vote
1
reply
639
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2
vst
cox-regression
Salmon
Tximport
updated 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
filippo.martignano
• 0
1
vote
6
replies
1.4k
views
Normalisation for count data visualisation only
deseq2
salmon
tximport
normalization
updated 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
Alex So
• 0
4
votes
10
replies
1.5k
views
what should I do with many zero counts from Salmon quantification
Salmon
DESeq2
normalization
r
updated 4.0 years ago by
Michael Love
39k • written 4.0 years ago by
lkianmehr
• 0
50 results • Page
1 of 1
Recent ...
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Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
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Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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