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
0
votes
14
replies
2.3k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
2.7 years ago Abhishek • 0
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
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
4
votes
10
replies
2.7k
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
5
votes
10
replies
11k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 6.1 years ago by 41k • written 6.2 years ago by ▴ 30
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
9
replies
5.3k
views
Trouble with Tximport
tximport salmon
updated 8.0 years ago by 41k • written 8.0 years ago by ▴ 30
1
vote
9
replies
2.5k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 5.0 years ago by ▴ 120 • written 5.0 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 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
2
votes
8
replies
1.6k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 5.0 years ago by 41k • written 5.0 years ago by • 0
6
votes
8
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 5 days ago by • 0 • written 14 months ago by ▴ 10
1
vote
8
replies
2.8k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
4.6 years ago k1m ▴ 20
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
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
0
votes
7
replies
1.9k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 2.9 years ago by 41k • written 3.2 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 5.8 years ago by 41k • written 5.8 years ago by ▴ 20
0
votes
6
replies
2.8k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
6.9 years ago sunil.mangalam • 0
0
votes
6
replies
1000
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 5.9 years ago by 25k • written 5.9 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
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
0
votes
6
replies
1.1k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 4.1 years ago by • 0 • written 4.1 years ago by • 0
1
vote
5
replies
3.1k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 5.9 years ago by 41k • written 6.9 years ago by • 0
0
votes
5
replies
1.2k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
4.3 years ago omid.alamdari • 0
5
votes
5
replies
4.8k
views
tximport transcript missing
deseq2 salmon tximport
4.7 years ago mr6518849 ▴ 10
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
5
replies
1.9k
views
tximport error with salmon version
deseq2 salmon tximport
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
1
vote
5
replies
1.8k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 7.5 years ago by 41k • written 7.5 years ago by • 0
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 15 months ago by • 0
0
votes
5
replies
1.4k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 3.7 years ago by 41k • written 3.7 years ago by • 0
0
votes
5
replies
1.9k
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 4.2 years ago by 41k • written 4.2 years ago by • 0
3
votes
4
replies
1.7k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 10
0
votes
4
replies
1.1k
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 4.0 years ago by 41k • written 4.0 years ago by • 0
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
1
vote
4
replies
1.3k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
7.8 years ago Assa Yeroslaviz ★ 1.5k
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
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
0
votes
4
replies
1.4k
views
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
6.7 years ago bruno.saubamea • 0
0
votes
4
replies
1.5k
views
Filtering output from tximport
tximport Salmon
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
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
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
0
votes
3
replies
400
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 6 months ago by 41k • written 6 months 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 41k • 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 2.3 years ago by • 0 • written 6.8 years ago by • 0
3
votes
3
replies
2.4k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth R salmon rna seq salmon
6.4 years ago Walter F. Baumann ▴ 10
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
0
votes
3
replies
4.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 5.9 years ago by ★ 2.0k • written 5.9 years ago by ▴ 30
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
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
3
replies
1.1k
views
DESeq2 gives weird results
deseq2 salmon
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Answer: A ComBat-seq issue: the covariates are confounded by ATpoint ★ 4.0k
```r > table(batch, group) group batch egfr gfp her2 1 0 12 5 2 6 6 0 ``` All of her2 is batch2, all of egfr i…
Votes
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
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