Showing : salmon • reset
16
votes
25
replies
3.9k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.9 years ago by ▴ 60
0
votes
14
replies
3.0k
views
Best practice for quantifying sncRNA
Salmon sncRNA RNASeq
3.6 years ago • updated 3.5 years ago Abhishek • 0
3
votes
12
replies
2.2k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
2
votes
11
replies
3.6k
views
Cannot find header.json in salmon index directory
salmon tximeta rna-seq
5.3 years ago • updated 5.2 years ago mico • 0
6
votes
10
replies
2.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 9 weeks ago by ★ 4.7k • written 11 weeks ago by ▴ 10
6
votes
10
replies
3.0k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 10 months ago by • 0 • written 2.0 years ago by ▴ 10
5
votes
10
replies
13k
views
Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Transcript Annotation
Michael Love Salmon tximport tx2gene
updated 7.0 years ago by 43k • written 7.0 years ago by ▴ 30
4
votes
10
replies
3.9k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
vote
9
replies
3.0k
views
error in aSwitchlist (isoformswitchanalyzeR)
isoformswitchanalyzeR tximport rnaseq salmon
updated 5.9 years ago by ▴ 120 • written 5.9 years ago by • 0
2
votes
9
replies
1.5k
views
Tximport of quasi-alignment-based RNAseq quantification (Salmon) for use with edgeR
salmon edger tximport rnaseq
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 20
5
votes
9
replies
6.0k
views
Trouble with Tximport
tximport salmon
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 30
5
votes
9
replies
3.9k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
7.0 years ago emmak ▴ 20
2
votes
8
replies
2.2k
views
Transcript variant analysis on Salmon output
Salmon RNA-Seq Transcript variant analysis
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
8
replies
3.5k
views
IgnoreTxVersion on Tximport not working
Tximport Salmon
5.4 years ago k1m ▴ 20
2
votes
7
replies
3.1k
views
tximport - using hg38 with RefSeq (NM) and Gene Symbol
salmon hg38 tximport tx2gene.csv
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
2
votes
7
replies
1.9k
views
Transcript abundance estimation for time-course RNA-seq data
rna-seq salmon alpine transcript expression
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 20
0
votes
7
replies
2.7k
views
Subtracting Background Signal Before DESeq Analysis
Salmon DESeq2
updated 3.7 years ago by 43k • written 4.0 years ago by ▴ 30
2
votes
7
replies
2.4k
views
RNA-seq with Salmon and tximport
RNA-seq Salmon tximport
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
6
replies
1.4k
views
Handling diploid vs haploid reference genomes in salmon > DESeq2 analysis
deseq2 salmon
updated 6.8 years ago by 25k • written 6.8 years ago by • 0
0
votes
6
replies
3.2k
views
Salmon, tximport and DeSeq2 for differential expression analysis of 3' biased data
tximport DESeq2 "tximport" deseq2 salmon
7.7 years ago sunil.mangalam • 0
0
votes
6
replies
1.4k
views
tximport lose transcript names with Salmon bootstrap
salmon tximport bootstrap
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
2
votes
6
replies
5.5k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
3.7 years ago • updated 3.6 years ago reganhayward • 0
2
votes
6
replies
2.3k
views
Normalisation for count data visualisation only
deseq2 salmon tximport normalization
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
4
votes
5
replies
740
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
3 months ago LuciaNhu • 0
5
votes
5
replies
5.7k
views
tximport transcript missing
deseq2 salmon tximport
5.6 years ago mr6518849 ▴ 10
0
votes
5
replies
1.8k
views
Error using DRIMSeq with Salmon count data
DRIMSeq tximport txdb Salmon
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
1
vote
5
replies
2.1k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
0
votes
5
replies
1.6k
views
importing salmon rnaseq quant with tximeta
tximeta salmon deseq2
5.1 years ago omid.alamdari • 0
0
votes
5
replies
2.4k
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 5.0 years ago by 43k • written 5.0 years ago by • 0
2
votes
5
replies
2.1k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 11 months ago by 43k • written 2.1 years ago by • 0
1
vote
5
replies
2.3k
views
tximport error with salmon version
deseq2 salmon tximport
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
vote
5
replies
3.2k
views
RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 70
1
vote
5
replies
3.6k
views
tximport using for data generated from other tools
tximport salmon eXpress
updated 6.8 years ago by 43k • written 7.7 years ago by • 0
12
votes
4
replies
4.6k
views
WGCNA following salmon/DESeq2
deseq2 wgcna salmon
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 30
0
votes
4
replies
662
views
Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
8 months ago JG13 • 0
9
votes
4
replies
3.9k
views
GC/length bias correction in gene expression quantification - Is CQN necessary if using Salmon --GCBias option?
salmon cqn tximport deseq2 rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 30
1
vote
4
replies
1.6k
views
comparing transcripts expression between conditions
salmon transcripts significance counts
8.6 years ago Assa Yeroslaviz ★ 1.5k
1
vote
4
replies
2.4k
views
tximport error reading salmon quantification files...
tximport salmon
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 20
1
vote
4
replies
1.7k
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 7.4 years ago by 43k • written 7.4 years ago by ▴ 30
0
votes
4
replies
1.5k
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 4.8 years ago by 43k • written 4.8 years ago by • 0
3
votes
4
replies
2.1k
views
quant.sf files and tximport, transcripts not recognized
salmon tximport
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
0
votes
4
replies
1.7k
views
How to deal with contaminating transcripts in TxImport/DESeq2?
deseq2 salmon tximport
7.5 years ago bruno.saubamea • 0
1
vote
4
replies
2.5k
views
processing of (salmon) gene counts for eqtl analysis
salmon tximport gene length eqtl TMM
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 120
0
votes
4
replies
2.0k
views
Filtering output from tximport
tximport Salmon
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
3
replies
1.8k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2 edgeR salmon tximport
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
vote
3
replies
1.9k
views
tximeta on STAR-aligned Salmon-quantified output
tximeta salmon STAR
updated 4.8 years ago by 43k • written 4.8 years ago by ▴ 10
2
votes
3
replies
2.9k
views
Getting between sample/within sample normalized gene expression values from DESeq2
rnaseq deseq2 tximport salmon normalization
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
votes
3
replies
902
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 16 months ago by 43k • written 16 months ago by • 0
4
votes
3
replies
3.8k
views
tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
tximport salmon R bioconductor
updated 3.1 years ago by • 0 • written 7.6 years ago by • 0
3
votes
3
replies
2.8k
views
Using sluth with Salmon data, error while sleuth_prep
sleuth R salmon rna seq salmon
7.3 years ago Walter F. Baumann ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Overcoming confounding in batch effect correction by Dario Strbenac ★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Comment: Overcoming confounding in batch effect correction by ATpoint ★ 4.7k
biostars.org and the [bioinformatics reddit][1] are suitable and have much larger audience than this forum here. [1]: https://www.reddi…
Comment: Overcoming confounding in batch effect correction by bbao ▴ 10
Thank you! And apologies for posting here. Do you know which forum I should go to in the future for questions like these?
Comment: For some reason I can't update BiocManager to 3.20 by shepherl 4.1k
interesting. it could be since this is not your installation that it was installed by an admin that you do not have access to perform this…
Comment: Overcoming confounding in batch effect correction by ATpoint ★ 4.7k
Hi, this is not related to Bioconductor directly. And no, you cannot correct anything because in your own batch you only have a single samp…
Votes
Answer: Store Matrix in DataFrame Cell
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
Comment: Overcoming confounding in batch effect correction
Overcoming confounding in batch effect correction
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