Showing : txImport • reset
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport dtu salmon TPM rnaseqDTU
written 5.1 years ago by ▴ 60
4
votes
13
replies
1.3k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 6 months ago by ▴ 40
6
votes
10
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
4
votes
9
replies
4.3k
views
How to get DESeq2 sizefactors from data imported using tximport
deseq2 sailfish tximport
updated 11 months ago by • 0 • written 6.8 years ago by • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
9 months ago Ndimensional ▴ 20
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
11 months ago Yijing • 0
1
vote
5
replies
2.8k
views
tximport error: all(txId == raw[[txIdCol]]) is not TRUE
tximport
updated 9 months ago by 41k • written 2.5 years ago by • 0
0
votes
5
replies
9.2k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 5 weeks ago by • 0 • written 7.6 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 16 months ago by • 0
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by ▴ 190 • written 3.8 years ago by ▴ 620
0
votes
4
replies
850
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 7 months ago by 41k • written 8 months ago by • 0
0
votes
3
replies
410
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
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
2
votes
3
replies
794
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
0
votes
2
replies
144
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 days ago Marianna ▴ 20
3
votes
2
replies
546
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 4 months ago by 65k • written 4 months ago by • 0
0
votes
2
replies
811
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago • updated 11 months ago Yijing • 0
0
votes
2
replies
191
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 29 days ago by 41k • written 29 days ago by • 0
0
votes
2
replies
642
views
tximport error in reading salmon output files?
tximport tximportData
updated 12 weeks ago by • 0 • written 10 months ago by • 0
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 9 months ago by ▴ 10
2
votes
1
reply
233
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 6 weeks ago by ★ 4.0k • written 6 weeks ago by • 0
0
votes
1
reply
592
views
Which file in tximport should I use for DESeq2 analysis?
tximport DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
2
votes
1
reply
639
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 11 months ago by 41k • written 11 months ago by • 0
0
votes
1
reply
319
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.0k • written 4 months ago by • 0
25 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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