Showing : salmon • reset
1
vote
2
replies
163
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
11 weeks ago • updated 10 weeks ago Nikolay Ivanov • 0
0
votes
5
replies
140
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 10 weeks ago by 32k • written 11 weeks ago by ▴ 10
0
votes
2
replies
91
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3 months ago by 56k • written 3 months ago by • 0
0
votes
5
replies
157
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 9 months ago by 32k • written 9 months ago by • 0
2
votes
1
reply
134
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 9 months ago by 32k • written 9 months ago by ▴ 20
2
votes
2
replies
111
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
10 months ago keremwai • 0
2
votes
3
replies
107
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 11 months ago by 32k • written 11 months ago by • 0
0
votes
3
replies
114
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 11 months ago by 32k • written 11 months ago by • 0
1
vote
3
replies
168
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 12 months ago by 32k • written 12 months ago by • 0
0
votes
4
replies
113
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 13 months ago by 32k • written 13 months ago by • 0
4
votes
0
replies
417
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
13 months ago Michael Love 32k
0
votes
6
replies
166
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 13 months ago by • 0 • written 14 months ago by • 0
0
votes
3
replies
193
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 15 months ago by 32k • written 15 months ago by • 0
0
votes
1
reply
142
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 15 months ago by 32k • written 15 months ago by • 0
0
votes
5
replies
117
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 15 months ago by 32k • written 15 months ago by • 0
0
votes
5
replies
156
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
16 months ago omid.alamdari • 0
2
votes
11
replies
795
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
18 months ago • updated 17 months ago mico • 0
1
vote
3
replies
171
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 18 months ago by 2.9k • written 18 months ago by ▴ 10
0
votes
8
replies
322
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
19 months ago k1mukund • 0
1
vote
2
replies
185
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 20 months ago by 32k • written 20 months ago by ▴ 10
2
votes
3
replies
199
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 20 months ago by 32k • written 20 months ago by • 0
2
votes
7
replies
437
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 20 months ago by 56k • written 20 months ago by • 0
1
vote
1
reply
248
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
20 months ago konstantinos.bogias ▴ 10
5
votes
5
replies
1.4k
views
tximport transcript missing
deseq2 salmon tximport
21 months ago mr6518849 ▴ 10
0
votes
2
replies
257
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 23 months ago by 32k • written 23 months ago by ▴ 20
1
vote
3
replies
226
views
DESeq2 gives weird results
deseq2 salmon
updated 23 months ago by 32k • written 23 months ago by • 0
1
vote
1
reply
502
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.0 years ago by 32k • written 2.3 years ago by ▴ 10
1
vote
9
replies
571
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 2.1 years ago by ▴ 100 • written 2.1 years ago by • 0
1
vote
5
replies
620
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
updated 2.1 years ago by 32k • written 2.1 years ago by ▴ 10
2
votes
8
replies
363
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 2.1 years ago by 32k • written 2.1 years ago by • 0
3
votes
4
replies
321
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 2.1 years ago by 32k • written 2.1 years ago by ▴ 10
1
vote
1
reply
307
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 2.1 years ago by 32k • written 2.1 years ago by • 0
1
vote
6
replies
676
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 2.2 years ago by 32k • written 2.2 years ago by • 0
4
votes
10
replies
502
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 2.3 years ago by 32k • written 2.3 years ago by • 0
1
vote
3
replies
521
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 2.3 years ago by 32k • written 2.3 years ago by • 0
8
votes
4
replies
1.2k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 2.5 years ago by ★ 2.6k • written 2.5 years ago by ▴ 10
2
votes
3
replies
490
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 2.5 years ago by 32k • written 2.5 years ago by ▴ 10
1
vote
1
reply
266
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 2.5 years ago by 32k • written 2.5 years ago by ▴ 10
0
votes
0
replies
329
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
2.5 years ago lkianmehr • 0
1
vote
2
replies
348
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
2.6 years ago fcuy047 • 0
2
votes
7
replies
532
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 2.8 years ago by 32k • written 2.8 years ago by ▴ 20
2
votes
9
replies
550
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 3.0 years ago by ★ 26k • written 3.0 years ago by ▴ 10
0
votes
3
replies
996
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 3.0 years ago by ★ 1.9k • written 3.0 years ago by ▴ 30
1
vote
1
reply
440
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 3.0 years ago by 56k • written 3.0 years ago by • 0
0
votes
6
replies
360
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 3.0 years ago by 25k • written 3.0 years ago by • 0
1
vote
5
replies
1.9k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 3.0 years ago by 32k • written 3.9 years ago by • 0
1
vote
4
replies
783
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 3.0 years ago by 32k • written 3.0 years ago by ▴ 120
0
votes
1
reply
393
views
tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 3.2 years ago by 32k • written 3.2 years ago by • 0
0
votes
2
replies
978
views
use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 3.2 years ago by 32k • written 3.2 years ago by • 0
5
votes
10
replies
5.4k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 3.2 years ago by 32k • written 3.2 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Effect of feature number on adjusted p-values by ATpoint ▴ 630
Wouldn't a proper DE analysis have a single count matrix with all involved genes and samples (or cell type, clusters, or whatever you analy…
Comment: Cannot install packages by BiocManager::install() by James • 0
Thanks so much for posting this! Have been going crazy all afternoon trying to install a package!
Answer: DiffBind by Rory Stark ★ 3.8k
I'll answer the second question first. You should not accessing the `$binding` matrix directly -- the chromosome names are factor numbers,…
Comment: How to download the ChAMP dependency ChAMPdata by shepherl 2.6k
You could try increasing the timeout limit for downloading files. I increased mine in a `.Rprofile` script so its persistent in all sessio…
Comment: DiffBind reporting error by Rory Stark ★ 3.8k
If you could give me access to your `dbind_de` object, I can have a look at what is going on. it would help to see the sequence of calls yo…
Votes
Bioconductor Award for Outstanding Documentation
C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
C: With DESeq2 "Not full rank" Error with design ~ line + time + condition
What does dba.PCA in DiffBind exactly do?
Answer: How to retrieve peak summit from DiffBind peaks
Awards • All
Teacher to Alejandro Reyes ★ 1.8k
Scholar to Aaron Lun ★ 26k
Prophet to ijvechetti • 0
Scholar to James W. MacDonald 56k
Scholar to Michael Love 32k
Locations • All
WEHI, Melbourne, Australia, 2 minutes ago
Australia, 9 minutes ago
United States, 10 minutes ago
Brazil, 16 minutes ago
Germany, 18 minutes ago
Traffic: 454 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