ChrisWills

# GNU Screen - main configuration file 
# All other .screenrc files will source this file to inherit settings.
# Author: Christian Wills - cwills.sys@gmail.com

# Allow bold colors - necessary for some reason
attrcolor b ".I"

# Tell screen how to set colors. AB = background, AF=foreground
termcapinfo xterm 'Co#256:AB=\E[48;5;%dm:AF=\E[38;5;%dm'

KartikTalwar

The fastest remote directory rsync over ssh archival I can muster (40MB/s over 1gb NICs)

This creates an archive that does the following:

rsync (Everyone seems to like -z, but it is much slower for me)

• a: archive mode - rescursive, preserves owner, preserves permissions, preserves modification times, preserves group, copies symlinks as symlinks, preserves device files.
• H: preserves hard-links
• A: preserves ACLs

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

mariozig

# Assume we are in your home directory
cd ~/

# Clone the repo from GitLab using the `--mirror` option
$ git clone --mirror git@your-gitlab-site.com:mario/my-repo.git

# Change into newly created repo directory
$ cd ~/my-repo.git

# Push to GitHub using the `--mirror` option.  The `--no-verify` option skips any hooks. 

PoisonAlien

__author__ = "Anand M"

'''
Takes output file generated by VarScan2 somatic programme and converts the formats.
'''

import argparse, math, re

parser = argparse.ArgumentParser(
    description="Converts VarScan2 somatic vcf to native format and vice-versa.\nInput is automatically detected")

PoisonAlien

# Usage
# 
# oncotate(maflite, header = FALSE, basename = NULL)
# Arguments
# 
# maflite	
# input tsv file with chr, start, end, ref_allele, alt_allele columns. (rest of the columns, if present will be attached to the output maf)
#
# header	
# logical. Whether input has a header line. Default is FALSE.

pierrejoubert73

How to add a collapsible section in markdown

1. Example

Click me

Heading

1. Foo
2. Bar
   • Baz

• Qux

sbamin

schochastics

#install UMAP from https://github.com/lmcinnes/umap
#install.packages("rPython")

umap <- function(x,n_neighbors=10,n_components=2,min_dist=0.1,metric="euclidean"){
  x <- as.matrix(x)
  colnames(x) <- NULL
  rPython::python.exec( c( "def umap(data,n,d,mdist,metric):",
                           "\timport umap" ,
                           "\timport numpy",
                           "\tembedding = umap.UMAP(n_neighbors=n,n_components=d,min_dist=mdist,metric=metric).fit_transform(data)",

ilevantis

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.