Showing : txImport • reset
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
23 days ago Marianna ▴ 20
0
votes
2
replies
194
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
2
votes
1
reply
236
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
325
views
tximport error with rsem files
rsem tximport
updated 4 months ago by ★ 4.0k • written 4 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
3
votes
2
replies
549
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
3
replies
414
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
10
votes
11
replies
1.9k
views
tximport error: vroom
tximport
updated 6 months ago by • 0 • written 6 months ago by ▴ 40
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
0
votes
4
replies
859
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
2
votes
3
replies
797
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 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 9 months ago by ▴ 120 • written 9 months ago by ▴ 10
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
0
votes
2
replies
646
views
tximport error in reading salmon output files?
tximport tximportData
updated 12 weeks ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
596
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
641
views
scaledTPM for DESeq2 using tximport
DESeq2 tximport
updated 11 months ago by 41k • written 11 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 • updated 11 months ago Yijing • 0
0
votes
2
replies
815
views
Error in H5Fopen
rhdf5 Rhdf5lib kallisto tximport
12 months ago Yijing • 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 days ago by • 0 • written 14 months ago by ▴ 10
2
votes
5
replies
1.3k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2 tximport counts Salmon
updated 9 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
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
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
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
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
25 results • Page 1 of 1
Recent ...
Replies
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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