| # -*- org-export-babel-evaluate: nil; org-export-allow-bind-keywords: t; -*- | |
| #+AUTHOR: Malcolm Cook; | |
| #+EMAIL: malcolm_cook@stowers.org | |
| #+OPTIONS: ':nil H:3 toc:3 num:t \n:nil @:t ::t |:t ^:nil -:nil f:t *:t <:t _:nil | |
| #+OPTIONS: email:T author:T creator:T timestamp:T | |
| #+STARTUP: showall | |
| #+STARTUP: showall | |
| #+PROPERTY: header-args:R :session *R:htmlwidgets** |
| imputeIR<-function(inPath | |
| ,outPath | |
| ,source='imputeIR' | |
| ,txNameFmt='ITR%07d' | |
| ,IGVHideGene=FALSE | |
| ,index=FALSE | |
| ,... | |
| ) { | |
| ## PURPOSE: Write GTF file to <outPath> as a version of GTF file | |
| ## <inPath> containing additional transcripts, one for every region |
| #!/usr/bin/env Rscript | |
| ' | |
| USAGE: cuffdiff_gtf_attributes --input=<inputGTF> [--output=outputGTF] | --help | |
| OPTIONS: | |
| -i --input=<inputGTF> the inputGTF | |
| -o --output=[outputGTF] the outputGTF | |
| EXAMPLE: | |
| > wget ftp://ftp.ensembl.org/pub/release-82/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.82.gtf.gz |
Author: National Cancer Institute
These methods were successful in our lab using prostate tissue and for our specific objectives. Investigators must be aware that they will need to tailor the following protocol for their own research objectives and tissue under study.
More than 10,000 Cells
If the amount of microdissected material is substantial (>10,000 cells) then any of the standard procedures for isolating DNA are acceptable.
Less than 10,000 Cells
| == 2015-03-13 21:48:51,169 main INFO This is EasyBuild 2.1.0dev (framework: 2.1.0dev, easyblocks: 2.1.0dev) on host mango.sgc.loc. | |
| == 2015-03-13 21:48:51,170 main INFO Command line: --modules-tool=Lmod --robot=/n/local/sce/EasyBuild-dev/easybuild-easyconfigs/easybuild/easyconfigs --try-toolchain="['goolf', '1.7.20']" biodeps-1.6-goolf-1.4.10-extended.eb | |
| == 2015-03-13 21:48:51,171 main INFO Using /tmp/eb-dqaqb2 as temporary directory | |
| == 2015-03-13 21:48:51,172 main.tools.robot INFO Using robot path(s): ['/n/local/sce/EasyBuild-dev/easybuild-easyconfigs/easybuild/easyconfigs'] | |
| == 2015-03-13 21:48:51,172 main.tools.robot INFO Prepended list of robot search paths with /tmp/eb-dqaqb2/tweaked_easyconfigs: ['/tmp/eb-dqaqb2/tweaked_easyconfigs', '/n/local/sce/EasyBuild-dev/easybuild-easyconfigs/easybuild/easyconfigs'] | |
| == 2015-03-13 21:48:51,177 main.filetools INFO Command /n/local/sce/apps/lmod/lmod/libexec/lmod found at /n/local/sce/apps/lmod/lmod/libexec/lmod | |
| == 2015-03-13 21:48:51,177 main.Lmod INFO Full path for |
| [[DEBUG]] Going to use /tmp/tmp3P1tRE as temporary directory | |
| [[DEBUG]] Output from modulecmd python help: sh: modulecmd: command not found | |
| [[DEBUG]] Output from lmod python help: Usage: module [options] sub-command [args ...] | |
| Options: | |
| -h -? -H --help This help message | |
| -s availStyle --style=availStyle Site controlled avail style: system | |
| (default: system) | |
| -D Program tracing written to stderr |
| subset.SummarizedExperiment<-function(x | |
| ,rowSubset=TRUE | |
| ,colSubset=TRUE | |
| ,assaySubset=TRUE | |
| ,drop=FALSE | |
| ,provenanceTrack=FALSE | |
| ,...) { | |
| ## PURPOSE: implement subsetting of SummarizedExperiments by | |
| ## rowSubset : expression in terms of the GRanges attributes (and | |
| ## its mcols meta-data) held in rowData |
| pvec2<-function(v, FUN, ..., mc.set.seed = TRUE, mc.silent = FALSE, | |
| mc.cores = getOption("mc.cores", 2L), mc.cleanup = TRUE | |
| ,combineFUN = `c` | |
| ) { | |
| ### AUTHOR: malcolm_cook@stowers.org | |
| ### PURPOSE: an improvement(?) on parallel:pvec which | |
| ### (1) does not require v to be a vector, rather, v must | |
| ### implement `[`, `length`. Thus, i.e. BioConductor List (including | |
| ### GRangesList) is supported. | |
| ### (2) uses `parallel:splitIndices` to compute indices into v |
| (defadvice dired-do-flagged-delete | |
| (around dired-do-flagged-delete activate) | |
| "Allows more aggressive control over recursive deletion policy: | |
| `dired-recursive-deletes` is set based on the current-prefix-arg: | |
| 4=>top (with confirmation) | |
| 16=>always (with confirmation) | |
| 64=>always (without confirmation)" | |
| (interactive "p") | |
| (let ((dired-recursive-deletes (case (car current-prefix-arg) | |
| (4 'top) |
| library(IRanges) # for: coverage, psetdiff, etc | |
| library(GenomicRanges) # for: readGappedAlignments, | |
| library(Rsamtools) # for: reading bam files scanBam, countBam etc | |
| library(rtracklayer) # for: track file IO (bed, wig, etc) | |
| library(sqldf) # for: querying dataframes using SQL\ | |
| bamTabulateGaps <- function(bamPath, | |
| bedPath=paste(gsub('.bam$','',bamPath),'.junctions.bed',sep=''), | |
| trackName=gsub('\\..*','',basename(bamPath)), | |
| trackLine=sprintf("track name=%s graphType=junctions",trackName), |