Showing : views • reset
1
vote
2
replies
420
views
How to apply a function to a RleViesList object?
Views IRanges GRanges RleList
updated 16 months ago by ★ 5.9k • written 16 months ago by ★ 1.5k
0
votes
2
replies
668
views
calculating TSS enrichment from ATACseq data
GenomicRanges Views ATACseq TSS
3.7 years ago tangming2005 ▴ 190
2
votes
4
replies
858
views
Ranges on AAStrings
AAString Views Biostrings
5.9 years ago tobias.kockmann ▴ 20
0
votes
1
reply
963
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 6.5 years ago by 16k • written 6.5 years ago by • 0
0
votes
3
replies
1.5k
views
The way to window over sequences of a DNAStringSet
biostrings window mask views
updated 7.2 years ago by 16k • written 7.2 years ago by ▴ 30
2
votes
10
replies
2.8k
views
Extract three types of intergenic regions
granges views annotation iranges
updated 7.3 years ago by ★ 1.7k • written 7.3 years ago by ▴ 50
0
votes
3
replies
813
views
View of subsequences corresponding granges on +ve strand and rev. complementary of seq on -ve strand.
Views granges grangeslist iranges
updated 7.3 years ago by 16k • written 7.3 years ago by ▴ 50
1
vote
2
replies
849
views
Summary statistics of RleListViews object
rle Views
8.0 years ago Sean Davis 21k
2
votes
5
replies
1.1k
views
making a RleViewsList object gets slow with many chromosomes
views iranges rle
8.0 years ago Janet Young ▴ 740
9 results • Page 1 of 1
Recent ...
Replies
Answer: collapseReplicates error after tximeta by Michael Love 39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2? by Michael Love 39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by Michael Love 39k
Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
Awards • All
Popular Question to Ryan • 0
Popular Question to Guido Hooiveld ★ 3.5k
Scholar to James W. MacDonald 62k
Commentator to Michael Love 39k
Popular Question to twtoal ▴ 10
Locations • All
The city by the bay, 2 minutes ago
Iran, 18 minutes ago
WEHI, Melbourne, Australia, 41 minutes ago
Bologna, 46 minutes ago
San Diego, 1 hour ago
Traffic: 193 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