Biostar Workflow

Showing : Workflow • reset

votes

replies

934

views

Bioconductor Workflow

updated 13 months ago by Gordon Smyth 47k • written 13 months ago by sarastew1994 • 0

votes

replies

669

views

ExperimentData Deprecation Software Release Workflow

15 months ago • updated 9 months ago shepherl 3.4k

votes

replies

1.0k

views

Workflow Software ExperimentData Deprecation

2.2 years ago • updated 21 months ago shepherl 3.4k

votes

replies

414

views

Software annotation experiment workflow

updated 2.5 years ago by shepherl 3.4k • written 2.5 years ago by gnanaprakash.s • 0

vote

replies

361

views

rnaseqGene workflow deseq2

updated 3.1 years ago by Michael Love 39k • written 3.1 years ago by Assa Yeroslaviz ★ 1.5k

votes

replies

2.2k

views

software error deseq2 workflow rnaseqGene

updated 3.6 years ago by Martin Morgan 25k • written 3.6 years ago by pavan-bioconductor • 0

votes

replies

622

views

RNA-Seq Workflow

updated 3.7 years ago by Gordon Smyth 47k • written 3.7 years ago by detroit.drive • 0

7 results • Page 1 of 1

Recent ...

Replies

Answer: struggling to create a heatmap by ATpoint ★ 2.1k

I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…

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…

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