Showing : tximport • reset
0
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4
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501
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Using tximport for kallisto aligned TOIL data
kallisto tximport TOIL
20 days ago • updated 9 days ago Nicholas • 0
0
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11
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814
views
Problems with oarfish + tximport + swish
fishpond tximport tximeta
updated 9 weeks ago by • 0 • written 10 weeks ago by • 0
6
votes
7
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3.4k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
updated 12 weeks ago by 52k • written 4.9 years ago by ▴ 20
1
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2
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669
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
4
votes
5
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879
views
DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
4 months ago LuciaNhu • 0
0
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2
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494
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 5 months ago by 43k • written 5 months ago by • 0
0
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2
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498
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tximport data import
tximport
updated 6 months ago by 43k • written 6 months ago by • 0
1
vote
2
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951
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
7 months ago grothmn • 0
1
vote
2
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2.4k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 9 months ago by ▴ 40 • written 5.4 years ago by • 0
0
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4
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709
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Create count matrix from multible quant sf files from different directories
tximportData tximport salmon
9 months ago JG13 • 0
2
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3
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1.9k
views
How to convert transcript counts to gene counts in R?
DESeq2 tximport
written 2.4 years ago by ▴ 50
6
votes
10
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3.2k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 11 months ago by • 0 • written 2.1 years ago by ▴ 10
0
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2
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666
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
11 months ago Marianna ▴ 20
13 results • Page 1 of 1
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Comment: Annotation package for Manduca sexta by GA ▴ 10
Thank you!
Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k
If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Votes
Looking for equivalent EPIC chip v1 vs. v2 annotation variables
Properly constructing a hypergeometric test
A: Is logFC a log2 fold change or some other base in scran::findMarkers
Comment: Error in retrieving clinical data
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