Showing : salmon • reset
1
vote
1
reply
85
views
TPM to raw counts
salmon DESeq2
updated 14 days ago by 13k • written 14 days ago by • 0
0
votes
4
replies
311
views
Filtering output from tximport
tximport Salmon
updated 8 weeks ago by 35k • written 9 weeks ago by • 0
2
votes
2
replies
300
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
4 months ago Qin ▴ 10
0
votes
2
replies
245
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 5 months ago by 35k • written 5 months ago by • 0
0
votes
14
replies
741
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
5 months ago Abhishek • 0
2
votes
6
replies
454
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
7 months ago reganhayward • 0
2
votes
1
reply
273
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 8 months ago by 35k • written 8 months ago by • 0
1
vote
2
replies
447
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
11 months ago Nikolay Ivanov • 0
0
votes
7
replies
534
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 7 months ago by 35k • written 11 months ago by ▴ 10
0
votes
2
replies
272
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 11 months ago by 58k • written 11 months ago by • 0
0
votes
5
replies
456
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 17 months ago by 35k • written 17 months ago by • 0
2
votes
1
reply
336
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 18 months ago by 35k • written 18 months ago by ▴ 20
2
votes
2
replies
335
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
18 months ago keremwai • 0
2
votes
3
replies
265
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 19 months ago by 35k • written 19 months ago by • 0
0
votes
3
replies
285
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 20 months ago by 35k • written 20 months ago by • 0
1
vote
3
replies
460
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 20 months ago by 35k • written 20 months ago by ▴ 10
0
votes
4
replies
278
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 21 months ago by 35k • written 21 months ago by • 0
4
votes
0
replies
767
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
21 months ago Michael Love 35k
0
votes
6
replies
353
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 22 months ago by • 0 • written 22 months ago by • 0
0
votes
3
replies
706
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 23 months ago by 35k • written 23 months ago by • 0
0
votes
1
reply
387
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 24 months ago by 35k • written 24 months ago by • 0
0
votes
5
replies
371
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 24 months ago by 35k • written 24 months ago by • 0
0
votes
5
replies
350
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
2.0 years ago omid.alamdari • 0
2
votes
11
replies
1.3k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
2.2 years ago • updated 2.1 years ago mico • 0
1
vote
3
replies
304
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 2.2 years ago by 3.4k • written 2.2 years ago by ▴ 10
0
votes
8
replies
884
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
2.3 years ago k1mukund • 0
1
vote
2
replies
310
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 2.3 years ago by 35k • written 2.3 years ago by ▴ 10
2
votes
3
replies
368
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 2.4 years ago by 35k • written 2.4 years ago by • 0
2
votes
7
replies
776
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 2.4 years ago by 58k • written 2.4 years ago by • 0
1
vote
1
reply
387
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
2.4 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
2.1k
views
tximport transcript missing
deseq2 salmon tximport
2.5 years ago mr6518849 ▴ 10
0
votes
2
replies
367
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 2.6 years ago by 35k • written 2.6 years ago by ▴ 20
1
vote
3
replies
369
views
DESeq2 gives weird results
deseq2 salmon
updated 2.6 years ago by 35k • written 2.6 years ago by • 0
1
vote
1
reply
702
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.7 years ago by 35k • written 3.0 years ago by ▴ 10
1
vote
9
replies
1.0k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 2.8 years ago by ▴ 100 • written 2.8 years ago by • 0
1
vote
5
replies
989
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
updated 2.8 years ago by 35k • written 2.8 years ago by ▴ 10
2
votes
8
replies
585
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 2.8 years ago by 35k • written 2.8 years ago by • 0
3
votes
4
replies
572
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 2.8 years ago by 35k • written 2.8 years ago by ▴ 10
1
vote
1
reply
449
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 2.8 years ago by 35k • written 2.8 years ago by • 0
1
vote
6
replies
1.1k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 2.9 years ago by 35k • written 2.9 years ago by • 0
4
votes
10
replies
826
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 3.0 years ago by 35k • written 3.0 years ago by • 0
1
vote
3
replies
788
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 3.0 years ago by 35k • written 3.0 years ago by • 0
8
votes
4
replies
1.7k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 3.2 years ago by ★ 2.6k • written 3.2 years ago by ▴ 20
2
votes
3
replies
698
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 3.2 years ago by 35k • written 3.2 years ago by ▴ 20
1
vote
1
reply
390
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 3.2 years ago by 35k • written 3.2 years ago by ▴ 10
0
votes
0
replies
472
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
3.2 years ago lkianmehr • 0
1
vote
2
replies
498
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
3.2 years ago fcuy047 • 0
2
votes
7
replies
703
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 3.5 years ago by 35k • written 3.5 years ago by ▴ 20
2
votes
9
replies
709
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 3.7 years ago by ★ 27k • written 3.7 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 3.7 years ago by ★ 1.9k • written 3.7 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: airway package not compatible with R version 4.1.2 (2021-11-01) by ATpoint ▴ 970
`data(airway)` is your friend. The CRAN error comes from the fact that it is not a CRAN package, not that it is a version problem itself.
Comment: airway package not compatible with R version 4.1.2 (2021-11-01) by Lluís Revilla Sancho ▴ 660
I think it would help if you try again to install it via `BiocManager::install("airway")` and report the exact text output (without quittin…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by Michael Love 35k
This looks as expected with the control genes centered on the x-axis (yes, these can have high variance, this is discussed in work by Risso…
Comment: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data by argonvibio • 0
Hello Michael, and thank you for your reply. I have done as you described, estimating size factors with controlGenes before DESeq, but the…
Answer: DiffBind issue: zero values for all peaks in one chromosome by Rory Stark ★ 4.3k
Losing the reads for one tissue on one chromosome doesn't sound too good! I notice that you are using `DiffBind_3.0`, which is out of da…
Votes
Emirical Bayesian shrinkage for dispertion/LFC estimation
C: Emirical Bayesian shrinkage for dispertion/LFC estimation
A: Emirical Bayesian shrinkage for dispertion/LFC estimation
Comment: airway package not compatible with R version 4.1.2 (2021-11-01)
Comment: universalmotif, question about enrich_motifs function and number of hits returne
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