Showing : salmon • reset
0
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4
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1.9k
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How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
8.5 years ago bruno.saubamea • 0
6
votes
10
replies
3.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
12
votes
4
replies
5.3k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by ▴ 30
0
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2
replies
1.6k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 3.0 years ago by • 0
2
votes
9
replies
1.9k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ▴ 20
0
votes
6
replies
3.6k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
8.6 years ago sunil.mangalam • 0
2
votes
2
replies
1.7k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
5.6 years ago keremwai • 0
0
votes
2
replies
1.4k
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
1
vote
5
replies
3.9k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 8.7 years ago by ★ 29k • written 8.7 years ago by ▴ 70
1
vote
5
replies
4.0k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 7.7 years ago by 43k • written 8.6 years ago by • 0
2
votes
3
replies
3.3k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 8.6 years ago by 43k • written 8.6 years ago by • 0
4
votes
3
replies
4.2k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 4.1 years ago by • 0 • written 8.5 years ago by • 0
1
vote
5
replies
2.6k
views
tximport error with salmon version
deseq2 salmon tximport
updated 8.5 years ago by 43k • written 8.5 years ago by • 0
1
vote
4
replies
2.0k
views
Can I combine quants from SE and PE reads from replicates of same sample in Salmon Quasi-mapping mode?
salmon tximport limma-voom
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 30
5
votes
10
replies
14k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 30
2
votes
3
replies
2.5k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 10
5
votes
9
replies
4.4k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
8.0 years ago emmak ▴ 20
1
vote
2
replies
3.5k
views
use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
1
reply
1.2k
views
tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
vote
4
replies
2.9k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 120
0
votes
6
replies
1.7k
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 7.7 years ago by 25k • written 7.7 years ago by • 0
1
vote
1
reply
1.6k
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
0
votes
3
replies
5.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 7.7 years ago by ★ 2.1k • written 7.7 years ago by ▴ 30
2
votes
7
replies
2.4k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 20
1
vote
2
replies
1.5k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
7.2 years ago fcuy047 • 0
1
vote
1
reply
1.3k
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
2
votes
3
replies
2.8k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 30
1
vote
3
replies
2.2k
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
1
vote
1
reply
1.9k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 6.7 years ago by 43k • written 7.0 years ago by ▴ 60
5
votes
10
replies
5.5k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
6
replies
2.7k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
1
vote
1
reply
1.5k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
3
votes
4
replies
2.5k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 10
2
votes
8
replies
2.9k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
16
votes
25
replies
4.7k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 6.8 years ago by ▴ 60
1
vote
9
replies
3.7k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 6.8 years ago by ▴ 120 • written 6.8 years ago by • 0
1
vote
3
replies
1.6k
views
DESeq2 gives weird results
deseq2 salmon
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
2
replies
1.5k
views
Importing Salmon counts with tximport with host and virus genomes
salmon tximport
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 50
5
votes
5
replies
6.3k
views
tximport transcript missing
deseq2 salmon tximport
6.5 years ago mr6518849 ▴ 10
4
votes
5
replies
1.5k
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
5
votes
9
replies
6.6k
views
Trouble with Tximport
tximport salmon
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 30
1
vote
4
replies
1.9k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
9.5 years ago Assa Yeroslaviz ★ 1.5k
1
vote
5
replies
2.4k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 9.3 years ago by 43k • written 9.3 years ago by • 0
9
votes
4
replies
4.5k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 30
2
votes
7
replies
3.5k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
1
vote
4
replies
2.7k
views
tximport error reading salmon quantification files...
tximport salmon
updated 8.9 years ago by 68k • written 8.9 years ago by ▴ 20
0
votes
1
reply
1.7k
views
salmon quantification - identical transcripts in fasta file
salmon
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 30
1
vote
2
replies
2.8k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 2.5 years ago by ▴ 120 • written 2.5 years ago by ▴ 10
6
votes
10
replies
4.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 21 months ago by • 0 • written 3.0 years ago by ▴ 10
3
votes
12
replies
3.1k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
94 results • Page 1 of 2
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Answer: Are individual-mouse-based statistics possible in CellChat? by ATpoint ★ 5.0k
Not a Bioconductor package, I commented on the crosspost at https://www.biostars.org/p/9617271/
Comment: DESeq2 - how to shrink LFC for pairwise comparisons having multiple groups by ATpoint ★ 5.0k
apeglm is more cumbersome than ashr as with apeglm the coefficients need to be explicitely available in the resultsNames.So, you need to re…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Votes
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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