Showing : tximport • reset
16
votes
25
replies
2.9k
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 6 months ago by 41k • written 7 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 4 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
846
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
408
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
793
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
20 days ago Marianna ▴ 20
3
votes
2
replies
545
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
806
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago • updated 11 months ago Yijing • 0
0
votes
2
replies
190
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 28 days ago by 41k • written 28 days ago by • 0
0
votes
2
replies
638
views
tximport error in reading salmon output files?
tximport tximportData
updated 11 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
591
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
636
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 11 months ago by 41k • written 11 months ago by • 0
0
votes
1
reply
317
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
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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