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
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 7 months ago by ▴ 40
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 14 days ago by • 0 • written 15 months ago by ▴ 10
4
votes
13
replies
1.4k
views
Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
tximport DESeq2
updated 7 months ago by 41k • written 8 months ago by • 0
4
votes
9
replies
4.4k
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
3
votes
2
replies
561
views
tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
tximport DESeq2
updated 5 months ago by 65k • written 5 months ago by • 0
3
votes
7
replies
1.1k
views
failed to use tximport for creating count matrix from kallisto
tximport kallisto
12 months ago Yijing • 0
2
votes
9
replies
1.2k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
10 months ago Ndimensional ▴ 20
2
votes
1
reply
246
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by • 0
2
votes
3
replies
1.2k
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
807
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
2
votes
1
reply
655
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 11 months ago by 41k • written 11 months ago by • 0
2
votes
5
replies
1.4k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 10 weeks ago by 41k • written 16 months ago by • 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
1
vote
2
replies
1.5k
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
0
votes
2
replies
166
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
0
votes
4
replies
1.2k
views
tximport importer isoform abundance
tximport
updated 11 months ago by ▴ 190 • written 3.9 years ago by ▴ 620
0
votes
1
reply
347
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
2
replies
206
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
0
votes
1
reply
610
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
0
votes
2
replies
664
views
tximport error in reading salmon output files?
tximport tximportData
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
880
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
0
votes
3
replies
427
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
0
votes
5
replies
9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 6 weeks ago by • 0 • written 7.6 years ago by • 0
24 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
France, 12 minutes ago
WEHI, Melbourne, Australia, 15 minutes ago
Sweden, 32 minutes ago
Japan, 51 minutes ago
EMBL Heidelberg, 1 hour ago
Traffic: 447 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6