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    45 repositories

    • Pipelines_INMEGEN

      Public
      Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.
      dockerfilebioinformaticssomatic-variantsvariant-callinggenomic-data-analysisnextflow-pipelinernaseq-analysistranscriptome-analysis
      Nextflow
      •0•9•0•0•Updated Nov 12, 2024Nov 12, 2024

    • Clase_pipelines

      Public
      Respositorio del curso "Aprende a utilizar los flujos de análisis bioinformáticos internos del Inmegen"
      HTML
      •0•3•0•0•Updated Oct 24, 2024Oct 24, 2024

    • CienciaDeDatosConR

      Public
      HTML
      •
      MIT License
      •1•7•0•0•Updated Sep 2, 2024Sep 2, 2024

    • MCAC

      Public
      Myocardiopathies and Arhythmogenic Channelopathies
      Shell
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Apr 22, 2024Apr 22, 2024

    • CovDif

      Public
      Software to compare conservation between groups of genomes
      Python
      •1•0•0•0•Updated Mar 8, 2022Mar 8, 2022

    • conservationLandscape

      Public
      This pipeline generates a conservation landscape based on kmer frequency
      Nextflow
      •0•0•0•0•Updated Apr 12, 2021Apr 12, 2021

    • ARPA

      Public
      AUTOMATIC RT-PCR DATA ANALYSIS FOR SARS-COV-2 DETECTION
      R
      •
      MIT License
      •0•1•0•0•Updated Feb 24, 2021Feb 24, 2021

    • mk_bwa_align

      Public
      sequence alignment with the BWA algorithm from FASTQ to a sorted and indexed .bam
      Makefile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 17, 2020Sep 17, 2020

    • UseR-INMEGEN-2019

      Public
      UseR! INMEGEN 2019
      0•0•0•0•Updated Oct 4, 2018Oct 4, 2018

    • fantom-series

      Public
      Time series analyses on fantom networks.
      Java
      •
      GNU General Public License v3.0
      •1•0•2•0•Updated Sep 13, 2018Sep 13, 2018

    • taller.supercomputo

      Public
      Repositorio con material del Curso-Taller Supercómputo en el INMEGEN
      Shell
      •
      GNU General Public License v3.0
      •14•9•0•0•Updated Aug 8, 2018Aug 8, 2018

    • ejercicios-mk

      Public
      Makefile
      •1•0•0•0•Updated Jul 12, 2018Jul 12, 2018

    • mk_breakdancer

      Public
      Genome-wide detection of structural variants by Breakdancer max in LSF
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 16, 2018Apr 16, 2018

    • mk-delly

      Public
      Makefile
      •0•0•0•0•Updated Mar 12, 2018Mar 12, 2018

    • mk-gatk

      Public
      Makefile
      •1•0•0•0•Updated Nov 26, 2017Nov 26, 2017

    • mk_freebayes_varcall

      Public
      Estimates variant call from indexed .bam files
      Makefile
      •
      Other
      •0•0•0•0•Updated Nov 10, 2017Nov 10, 2017

    • mk-Crossmap

      Public
      Module for converting genome coordinates between diferent genome versions. Works in vcf, bam, bed, bigwig, gff, wig formats.
      Makefile
      •0•0•0•0•Updated Nov 9, 2017Nov 9, 2017

    • VEP_VCF-annotator

      Public
      MK for Variant annotation using VEP
      Makefile
      •0•0•0•0•Updated Oct 4, 2017Oct 4, 2017

    • vcf_bed_filter

      Public
      Call variants of a bed file from a vcf file using bcftools.
      Makefile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 3, 2017Oct 3, 2017

    • mk_cols_sum

      Public
      Designed for sum RNAseq counts from paired and unpaired readings, this mk uses awk to sum two columns from two different files whit the same record number.
      Makefile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 8, 2017Aug 8, 2017

    • mk_rmdup

      Public
      Remove potential PCR duplicates using samtools rmdup.
      Makefile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 18, 2017Jul 18, 2017

    • mk-indexbam

      Public
      Index a bunch of bam files using samtools
      Makefile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 18, 2017Jul 18, 2017

    • ejemplo-pipeline

      Public
      0•0•0•0•Updated Jul 6, 2017Jul 6, 2017

    • proyecto-vacio

      Public
      Makefile
      •0•0•0•0•Updated Jul 6, 2017Jul 6, 2017

    • comorbilidad

      Public
      Awk
      •0•0•0•0•Updated Jul 3, 2017Jul 3, 2017

    • 100g

      Public
      100 amerindian genomes
      Shell
      •
      GNU General Public License v3.0
      •1•1•1•0•Updated Jun 28, 2017Jun 28, 2017

    • fastqc_summary

      Public
      R
      •0•0•0•0•Updated Jun 2, 2017Jun 2, 2017

    • mk-angsd

      Public
      Pipeline for population Branch statistics calculation
      Makefile
      •0•0•0•0•Updated May 20, 2017May 20, 2017

    • snpEff_VCF-annotator

      Public
      Annotate variants from a VCF, using a MK script.
      0•0•0•0•Updated May 19, 2017May 19, 2017

    • sortindexvcf

      Public
      sort index VCFs
      Makefile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 25, 2017Apr 25, 2017