Alternatives and similar repositories for gcp-for-bioinformatics

Users that are interested in gcp-for-bioinformatics are comparing it to the libraries listed below

• lynnlangit / aws-for-bioinformatics
  AWS for Bioinformatics Researchers
  ☆148Updated 9 months ago
• lynnlangit / TeamTeri
  Bioinformatics on GCP, AWS or Azure
  ☆57Updated 2 months ago
• rnnh / bioinfo-notebook
  🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.
  ☆175Updated 4 years ago
• google / deepsomatic
  DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing …
  ☆172Updated 3 weeks ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆471Updated 2 months ago
• broadinstitute / genomics-in-the-cloud
  Source code and related materials for the O'Reilly book
  ☆94Updated 2 years ago
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆397Updated this week
• openwdl / learn-wdl
  Educational materials for learning WDL
  ☆125Updated last year
• nextflow-io / training
  Nextflow training material
  ☆171Updated this week
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆341Updated 10 months ago
• hbctraining / Intro-to-rnaseq-hpc-O2
  This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
  ☆170Updated 4 years ago
• hbctraining / Intro-to-DGE
  ☆197Updated 2 months ago
• pachterlab / ffq
  A tool to find sequencing data and metadata from public databases.
  ☆576Updated 9 months ago
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆446Updated this week
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆369Updated 2 weeks ago
• nextflow-io / patterns
  A curated collection of Nextflow implementation patterns
  ☆359Updated last year
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆252Updated 4 months ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆196Updated last month
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆442Updated last year
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆387Updated 5 months ago
• nf-core / tools
  Python package with helper tools for the nf-core community.
  ☆259Updated this week
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆422Updated last month
• pcingola / SnpEff
  ☆277Updated 3 months ago
• rpetit3 / fastq-dl
  Download FASTQ files from SRA or ENA repositories.
  ☆331Updated 2 months ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• broadinstitute / warp
  WDL Analysis Research Pipelines
  ☆211Updated this week
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆432Updated last year
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆329Updated 3 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆441Updated 3 weeks ago