rob-p

#!/usr/bin/env bash
pn=$1
convert $1 $1.ps
gs -dPDFA -dBATCH -dNOPAUSE -dNOOUTERSAVE -dUseCIEColor -sProcessColorModel=DeviceCMYK -sDEVICE=pdfwrite -sPDFACompatibilityPolicy=1 -sOutputFile=$1.a.pdf $1.ps

evd0kim

# License: MIT

import socket
from slacker import Slacker
import datetime
import time
import threading

SLACK_TOKEN = 'xoxb-00000000000-000000000000-000000000000000000000000'
CHANNEL_NAME = "your-channel-on-slack"

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.

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)",

sbamin

pierrejoubert73

How to add a collapsible section in markdown

1. Example

Click me

Heading

1. Foo
2. Bar
   • Baz

• Qux

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.

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")

mariozig

# Assume we are in your home directory
cd ~/

# Clone the repo from GitLab using the `--mirror` option
$ git clone --mirror [email protected]: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. 

davfre

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (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)