Alternatives and similar repositories for pandasVCF

Users that are interested in pandasVCF are comparing it to the libraries listed below

• openvax / varcode
  Library for manipulating genomic variants and predicting their effects
  ☆85Updated last year
• nellore / rail
  Scalable RNA-seq analysis
  ☆73Updated 5 years ago
• brentp / cruzdb
  python access to UCSC genomes database
  ☆136Updated 5 years ago
• slowkow / pytabix
  Retrieve data in genomic intervals with a Python interface for tabix.
  ☆82Updated 8 years ago
• BD2KGenomics / toil-scripts
  Toil workflows for common genomic pipelines
  ☆33Updated 6 years ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆89Updated 6 years ago
• schatzlab / appliedgenomics2017
  JHU EN.600.649: Computational Genomics: Applied Comparative Genomics
  ☆59Updated 7 years ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆84Updated 4 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 4 years ago
• BD2KGenomics / toil-rnaseq
  UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
  ☆41Updated 5 years ago
• KHP-Informatics / ngseasy
  Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
  ☆86Updated 8 years ago
• broadinstitute / oncotator
  ☆69Updated 3 years ago
• DaehwanKimLab / hisat
  Fast spliced aligner with low memory requirements
  ☆41Updated 10 years ago
• arq5x / cyvcf
  A fast Python library for VCF files leveraging Cython for speed.
  ☆52Updated 7 years ago
• ueser / FIDDLE
  Flexible Integration of Data with Deep LEarning
  ☆51Updated 2 years ago
• macarthur-lab / clinvar
  This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file…
  ☆131Updated 5 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆126Updated 9 months ago
• ding-lab / hotspot3d
  3D hotspot mutation proximity analysis tool
  ☆52Updated 2 years ago
• phenopolis / phenopolis
  An Open Platform for Harmonisation & Analysis of Sequencing & Phenotype Data
  ☆33Updated 3 years ago
• GenomiqueENS / dockerfiles
  ☆82Updated 3 years ago
• NCBI-Hackathons / Community_Software_Tools_for_NGS
  ☆63Updated 9 years ago
• griffithlab / pVAC-Seq
  DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools
  ☆61Updated 6 years ago
• WGLab / icages
  iCAGES (integrated CAncer GEnome Score) is an effective tool for prioritizing cancer driver genes for a patient
  ☆14Updated 3 years ago
• konstantint / pyliftover
  Pure-python implementation of UCSC liftOver genome coordinate conversion
  ☆101Updated 2 years ago
• gatk-workflows / five-dollar-genome-analysis-pipeline
  Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
  ☆57Updated 6 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• Clinical-Genomics / chanjo
  Chanjo provides a better way to analyze coverage data in clinical sequencing.
  ☆50Updated this week
• lgautier / fastq-and-furious
  Efficient handling of FASTQ files from Python
  ☆51Updated 2 months ago
• babelomics / babelomics
  ☆42Updated 7 years ago