Bioconductor Granges

Showing : granges • reset

votes

replies

2.7k

views

overlap snps granges iranges

updated 11.1 years ago by Michael Lawrence ★ 11k • written 11.1 years ago by anastasiya-terskih ▴ 10

votes

1.5k

views

Granges IRanges gff import.gff3 strand

updated 11.1 years ago by Hervé Pagès 16k • written 11.1 years ago by topher.hamm • 0

votes

replies

7.2k

views

GRanges seqnames seqlengths IRanges

11.1 years ago topher.hamm • 0

votes

replies

2.3k

views

granges

updated 11.1 years ago by Sean Davis 21k • written 11.1 years ago by Asma rabe ▴ 290

votes

2.7k

views

biostrings bsgenome granges

updated 11.1 years ago by Martin Morgan 25k • written 11.1 years ago by Miskey, Csaba ▴ 20

vote

replies

1.9k

views

GRanges GRangesList ChIP

11.1 years ago patrick.schordert ▴ 30

206 results • Page 5 of 5

Recent ...

Replies

Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

Votes

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Awards • All