Showing : Salmon • reset
16
votes
25
replies
2.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.0 years ago by ▴ 60
12
votes
4
replies
3.8k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by ▴ 30
9
votes
4
replies
3.3k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 7.1 years ago by 41k • written 7.1 years ago by ▴ 30
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 9 hours ago by • 0 • written 14 months ago by ▴ 10
5
votes
9
replies
3.4k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
6.2 years ago emmak ▴ 20
5
votes
5
replies
4.8k
views
tximport transcript missing
deseq2 salmon tximport
4.7 years ago mr6518849 ▴ 10
5
votes
9
replies
5.3k
views
Trouble with Tximport
tximport salmon
updated 8.0 years ago by 41k • written 8.0 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 41k • written 6.2 years ago by ▴ 30
4
votes
10
replies
2.8k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 5.2 years ago by 41k • written 5.2 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 2.3 years ago by • 0 • written 6.8 years ago by • 0
4
votes
1
reply
1.1k
views
Adding custom transcript to Salmon index
salmon
updated 20 months ago by ★ 4.0k • written 20 months ago by ▴ 20
4
votes
0
replies
2.0k
views
Tutorial: How to post Salmon data to GEO for use with tximeta
salmon tximeta Tutorial
4.0 years ago Michael Love 41k
3
votes
4
replies
1.7k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 10
3
votes
12
replies
1.4k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 12 months ago by 41k • written 12 months ago by ▴ 10
3
votes
3
replies
2.4k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth R salmon rna seq salmon
6.5 years ago Walter F. Baumann ▴ 10
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 41k • written 6.9 years ago by • 0
2
votes
6
replies
4.5k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
2.8 years ago reganhayward • 0
2
votes
7
replies
2.6k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.1 years ago by 41k • written 7.1 years ago by • 0
2
votes
1
reply
1.4k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 3.7 years ago by 41k • written 3.7 years ago by ▴ 20
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 5.4 years ago by 41k • written 5.4 years ago by ▴ 30
2
votes
6
replies
1.9k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
2
votes
3
replies
909
views
Error using tximport on Salmon with sparseMatrix on scaledTPM option
tximport Salmon sparse
updated 3.9 years ago by 41k • written 3.9 years ago by • 0
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 41k • written 5.1 years ago by • 0
2
votes
1
reply
653
views
Confused about tximport-DESeq2 setup
DESeq2 tximport salmon
updated 15 months ago by ★ 4.0k • written 15 months ago by • 0
2
votes
2
replies
2.0k
views
Volcano plots of DEGs from Swish are weird
DESeq2 fishpond salmon swish
2.6 years ago Qin ▴ 10
2
votes
9
replies
1.3k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
2
votes
7
replies
2.0k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 4.6 years ago by 65k • written 4.6 years ago by • 0
2
votes
3
replies
1.3k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 4.6 years ago by 41k • written 4.6 years ago by • 0
2
votes
7
replies
1.6k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 5.8 years ago by 41k • written 5.8 years ago by ▴ 20
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 8 weeks ago by 41k • written 16 months ago by • 0
2
votes
1
reply
1.0k
views
Salmon and DEseq2 - analysis of libraries saturated with ncRNAs
RNASeq Salmon DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
2
votes
11
replies
3.0k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
4.4 years ago mico • 0
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.8 years ago keremwai • 0
1
vote
3
replies
839
views
RNAseq PCA resembles subject-specific effect in a paired study design
salmon DESeq2
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by ▴ 10
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 6.6 years ago by 41k • written 6.6 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
1
vote
2
replies
2.1k
views
Regarding transcripts to gene ID conversion in tximport
salmon tximport DESeq2
3.2 years ago • updated 3.1 years ago Nikolay Ivanov • 0
1
vote
4
replies
2.0k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 120
1
vote
4
replies
2.1k
views
tximport error reading salmon quantification files...
tximport salmon
updated 7.1 years ago by 65k • written 7.1 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Controlling for batch after Salmon-Tximport
deseq2 wgcna salmon rna-seq DESeq2
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
1
vote
2
replies
2.8k
views
TPM to raw counts
salmon DESeq2
updated 4 months ago by • 0 • written 2.3 years ago by • 0
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
1
vote
2
replies
1.0k
views
What is the expected location of bootstrap samples relative to quant.sf file ?
tximport tximportdata salmon
5.5 years ago fcuy047 • 0
1
vote
5
replies
2.6k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 70
1
vote
2
replies
1.4k
views
IsoformSwitchAnalyzeR: What are the SV values created in design matrix?
salmon IsoformSwitchAnalyzeR tximport RNASeqData
updated 8 months ago by ▴ 120 • written 8 months ago by ▴ 10
1
vote
3
replies
1.5k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 3.9 years ago by 41k • written 3.9 years ago by ▴ 10
1
vote
1
reply
875
views
DEseq2 with different fastq read numbers after salmon
deseq2 salmon rna seq salmon
updated 5.4 years ago by 41k • written 5.4 years ago by ▴ 10
1
vote
3
replies
1.6k
views
Using Salmon and DESeq2 to compare metagenomic content between samples
salmon deseq2
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
1
vote
1
reply
1.3k
views
rnaseqDTU log2fold change DEXSeq
DEXSeq DTU salmon rnaseqDTU foldchange
updated 5.0 years ago by 41k • written 5.3 years ago by ▴ 60
1
vote
1
reply
986
views
Doubts about: Salmon -> Tximport -> Deseq2(vst) -> cox-regression
deseq2 vst cox-regression Salmon Tximport
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
Comment: DESeq filtering specific to contrasts by Michael Love 41k
It will likely not filter it out, but really the per-dataset details would affect the results.
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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