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adj2cytoscape

Convert the optput.adj from aracne to columm space delimited format ready to cytoscape

bioinformatics

Material para cursos de Bioinformática

ctx2vep

Extracts the necessary columns in the output of BreakDance to submit them to VEP

documentacion

extendalign

A computational algorithm for delivering multiple global alignment results originated from local alignments.

fastqc

csf fork of fastqc for usage on selected reads of unaligned bam file

flat-terminal

Flat design colours applied to terminal. Terminal is now sweeter than ever!

gitignore

A collection of useful .gitignore templates

gnu_linux_connecting_tools

Herramientas para uso a distancia de sistemas GNU/Linux

indexvcf

mergevcfs

mk-adj2sif

automation with mk of the transformation of ARACNe files to sif files

mk-annotation

mk automation of annovar annotation using cosmic db

mk-bwa-mem

mk automatization BWA MEM align, BAM convert, Picard sort and samtools index

mk-corto

MK automation of corto

mk-ena-submiter

MK automatization submit reads to European Nucleotide Archive using Webin command line submission interface

mk-extendalign

mk automatic workflow for EA in the INMEGEN

mk-extract-sra

MK automation of sra to fastq conversion with fasterq-dump

mk-mappedto23andme

mk automatization to convert .map .ped plink format to so called "23 and me" format

mk-parallel-aracne

ARACNe parallel and automaticed

mk-singlecell-workflow

Single cell workflow using ddSeeker and Drop-seq tools

mk-trimgalore

MK-trim galore, a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files.

mk-vcfdecompose

Decompose VCF using RTG Tools vcfdecompose

mk_addreadgroups

Add read groups to a group of .bam files using Picard

mk_concatvcf

Sort and concat VCFs usin bcftools

mk_corto_network

Correlation TF network using corto and MK

mk_daymet_mx_mun_daily

extract daymet daily info for Mexican municipalities

mk_daymet_mx_mun_mont

extract daymet mont average info for mx municipal

mkbreakdancerlsf

Genome-wide detection of structural variants by Breakdancer max in LSF

mkgetdepths

extract depth from a bunch of bams