Showing : Salmon • reset
0
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4
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1.4k
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How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
6.8 years ago bruno.saubamea • 0
0
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2
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956
views
tximport no counts from abundance using EnsDb.Hsapiens.v86
salmon EnsDb.Hsapiens.v86 tximport
updated 3.3 years ago by 66k • written 3.3 years ago by • 0
2
votes
9
replies
1.3k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 20
0
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6
replies
2.9k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
7.0 years ago sunil.mangalam • 0
2
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2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.9 years ago keremwai • 0
12
votes
4
replies
3.9k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 5.5 years ago by ★ 3.0k • written 5.5 years ago by ▴ 30
0
votes
2
replies
832
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 16 months ago by • 0
0
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1
reply
1.2k
views
salmon quantification - identical transcripts in fasta file
salmon
updated 7.1 years ago by 66k • written 7.1 years ago by ▴ 30
1
vote
5
replies
2.7k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 70
1
vote
5
replies
3.2k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 6.0 years ago by 42k • written 7.0 years ago by • 0
2
votes
3
replies
2.5k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
4
votes
3
replies
3.4k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 2.4 years ago by • 0 • written 6.9 years ago by • 0
1
vote
5
replies
2.0k
views
tximport error with salmon version
deseq2 salmon tximport
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
1
vote
4
replies
1.4k
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 6.7 years ago by 42k • written 6.7 years ago by ▴ 30
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.2 years ago by 42k • written 6.2 years ago by ▴ 30
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
5
votes
9
replies
3.5k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.3 years ago emmak ▴ 20
0
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2
replies
2.4k
views
use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
0
votes
1
reply
873
views
tximport error with Salmon in DESeq2 pipeline
tximport deseq2 salmon
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
1
vote
4
replies
2.1k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 6.1 years ago by 42k • written 6.1 years ago by ▴ 120
0
votes
6
replies
1.0k
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 6.0 years ago by 25k • written 6.0 years ago by • 0
1
vote
1
reply
1.2k
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 6.0 years ago by 66k • written 6.0 years ago by • 0
0
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3
replies
4.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 6.0 years ago by ★ 2.0k • written 6.0 years ago by ▴ 30
2
votes
7
replies
1.6k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 5.9 years ago by 42k • written 5.9 years ago by ▴ 20
1
vote
2
replies
1.1k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
5.6 years ago fcuy047 • 0
1
vote
1
reply
899
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 10
0
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3
replies
455
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 7 months ago by 42k • written 7 months ago by • 0
5
votes
9
replies
5.4k
views
Trouble with Tximport
tximport salmon
updated 8.1 years ago by 42k • written 8.1 years ago by ▴ 30
1
vote
4
replies
1.4k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
7.9 years ago Assa Yeroslaviz ★ 1.5k
1
vote
5
replies
1.8k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 7.6 years ago by 42k • written 7.6 years ago by • 0
9
votes
4
replies
3.4k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.2 years ago by 42k • written 7.2 years ago by ▴ 30
2
votes
7
replies
2.7k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.2 years ago by 42k • written 7.2 years ago by • 0
1
vote
4
replies
2.1k
views
tximport error reading salmon quantification files...
tximport salmon
updated 7.2 years ago by 66k • written 7.2 years ago by ▴ 20
0
votes
3
replies
326
views
Interaction tests and paired interaction tests in swish
swish salmon fishpond
updated 3 months ago by 42k • written 3 months ago by • 0
0
votes
4
replies
1.6k
views
Filtering output from tximport
tximport Salmon
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
1
vote
2
replies
1.6k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 9 months ago by ▴ 120 • written 9 months ago by ▴ 10
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 weeks ago by • 0 • written 15 months ago by ▴ 10
3
votes
12
replies
1.5k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 13 months ago by 42k • written 13 months ago by ▴ 10
1
vote
3
replies
1.6k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.0 years ago by 42k • written 4.0 years ago by ▴ 10
2
votes
3
replies
1.7k
views
GC content correction in salmon/deseq2 workflow for single-end RNAseq data
salmon edaseq rna-seq deseq2
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 30
1
vote
3
replies
1.6k
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
1
vote
1
reply
1.4k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 5.1 years ago by 42k • written 5.4 years ago by ▴ 60
4
votes
10
replies
2.9k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
2
votes
6
replies
2.0k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
1
vote
1
reply
1.0k
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 5.1 years ago by 42k • written 5.2 years ago by • 0
3
votes
4
replies
1.7k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 10
2
votes
8
replies
1.6k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
16
votes
25
replies
3.1k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
1
vote
9
replies
2.6k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 5.1 years ago by ▴ 120 • written 5.1 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq2 gives weird results
deseq2 salmon
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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