Showing : Salmon • reset
2
votes
2
replies
164
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
15 days ago • updated 4 days ago Qin ▴ 10
0
votes
2
replies
137
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 4 weeks ago by 34k • written 4 weeks ago by • 0
0
votes
14
replies
510
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
8 weeks ago • updated 7 weeks ago Abhishek • 0
2
votes
6
replies
307
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3 months ago reganhayward • 0
2
votes
1
reply
203
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 4 months ago by 34k • written 4 months ago by • 0
1
vote
2
replies
312
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
7 months ago Nikolay Ivanov • 0
0
votes
7
replies
394
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 3 months ago by 34k • written 7 months ago by ▴ 10
0
votes
2
replies
198
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 7 months ago by 58k • written 7 months ago by • 0
0
votes
5
replies
285
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 13 months ago by 34k • written 13 months ago by • 0
2
votes
1
reply
245
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 14 months ago by 34k • written 14 months ago by ▴ 20
2
votes
2
replies
237
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
15 months ago keremwai • 0
2
votes
3
replies
198
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 15 months ago by 34k • written 15 months ago by • 0
0
votes
3
replies
208
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 16 months ago by 34k • written 16 months ago by • 0
1
vote
3
replies
334
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 16 months ago by 34k • written 16 months ago by ▴ 10
0
votes
4
replies
209
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 17 months ago by 34k • written 17 months ago by • 0
4
votes
0
replies
603
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
17 months ago Michael Love 34k
0
votes
6
replies
254
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 18 months ago by • 0 • written 18 months ago by • 0
0
votes
3
replies
461
views
"lexical error: invalid char in json text" when using tximport
tximport salmon
updated 20 months ago by 34k • written 20 months ago by • 0
0
votes
1
reply
275
views
Salmon/DESeq2: tx2gene discrepancy in DESeq object
deseq2 tximport salmon
updated 20 months ago by 34k • written 20 months ago by • 0
0
votes
5
replies
262
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 20 months ago by 34k • written 20 months ago by • 0
0
votes
5
replies
259
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
20 months ago omid.alamdari • 0
2
votes
11
replies
1.1k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
22 months ago • updated 21 months ago mico • 0
1
vote
3
replies
261
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 23 months ago by 3.4k • written 23 months ago by ▴ 10
0
votes
8
replies
566
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
2.0 years ago k1mukund • 0
1
vote
2
replies
257
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 2.0 years ago by 34k • written 2.0 years ago by ▴ 10
2
votes
3
replies
290
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 2.0 years ago by 34k • written 2.0 years ago by • 0
2
votes
7
replies
595
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 2.1 years ago by 58k • written 2.1 years ago by • 0
1
vote
1
reply
327
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
2.1 years ago konstantinos.bogias ▴ 10
5
votes
5
replies
1.8k
views
tximport transcript missing
deseq2 salmon tximport
2.2 years ago mr6518849 ▴ 10
0
votes
2
replies
325
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 2.3 years ago by 34k • written 2.3 years ago by ▴ 20
1
vote
3
replies
313
views
DESeq2 gives weird results
deseq2 salmon
updated 2.3 years ago by 34k • written 2.3 years ago by • 0
1
vote
1
reply
638
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 2.4 years ago by 34k • written 2.7 years ago by ▴ 10
1
vote
9
replies
822
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 2.5 years ago by ▴ 100 • written 2.5 years ago by • 0
1
vote
5
replies
829
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 10
2
votes
8
replies
492
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 2.5 years ago by 34k • written 2.5 years ago by • 0
3
votes
4
replies
438
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 10
1
vote
1
reply
383
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 2.5 years ago by 34k • written 2.5 years ago by • 0
1
vote
6
replies
900
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 2.5 years ago by 34k • written 2.5 years ago by • 0
4
votes
10
replies
697
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 2.7 years ago by 34k • written 2.7 years ago by • 0
1
vote
3
replies
662
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 2.7 years ago by 34k • written 2.7 years ago by • 0
8
votes
4
replies
1.5k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 2.8 years ago by ★ 2.6k • written 2.8 years ago by ▴ 20
2
votes
3
replies
597
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 2.8 years ago by 34k • written 2.8 years ago by ▴ 20
1
vote
1
reply
326
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 2.8 years ago by 34k • written 2.8 years ago by ▴ 10
0
votes
0
replies
409
views
quantifying piRNA and tRNA by Salmon
Salmon DGE
2.9 years ago lkianmehr • 0
1
vote
2
replies
435
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
2.9 years ago fcuy047 • 0
2
votes
7
replies
639
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 3.2 years ago by 34k • written 3.2 years ago by ▴ 20
2
votes
9
replies
645
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 3.3 years ago by ★ 27k • written 3.3 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by ▴ 30
1
vote
1
reply
530
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 3.4 years ago by 58k • written 3.4 years ago by • 0
0
votes
6
replies
470
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 3.4 years ago by 25k • written 3.4 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Correct annotation of DGEList object from edgeR package regarding an RNA-Seq dat by IIart.hubII • 0
What is "coad_clear" in this case? What data have you allotted to it? Can you please share the whole code? Or can anyone answer this questi…
Comment: GenomicScores package: availableGScores and getGScores functions not working by Robert Castelo ★ 2.7k
hi, Indeed you were using an outdated version of the package. Regarding how to install current release version, please read first carefull…
Answer: Unable to install Bioconductor packages by shepherl 2.8k
This normally occurs when R was installed with a different account or an admin account. Unless on this account you won't be able to update…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
I tried to install the latest version of GenomicScores (2.4.0) by downloading the tar.gz and running `install.packages('GenomicScores_2.4.0…
Comment: GenomicScores package: availableGScores and getGScores functions not working by nattzy94 • 0
Thanks for the quick response. Below is my sessionInfo R version 3.6.2 (2019-12-12) Platform: x86_64-apple-darwin15.6.0 (64-bit) …
Votes
A: Differential expression analysis starting from TPM data
Comment: deseq2 machine sizing best practices for very large data set
Comment: Extracting normalized counts in MEDIPS
Comment: "full model matrix is less than full rank"
A: Extracting normalized counts in MEDIPS
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