Alternatives and similar repositories for pypiper

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

• pepkit / peppy
  Project metadata manager for PEPs in Python
  ☆37Updated 8 months ago
• czbiohub-sf / cerebra
  A tool for fast and accurate summarizing of variant calling format (VCF) files
  ☆60Updated 2 years ago
• brentp / python-giggle
  python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.
  ☆16Updated 7 years ago
• panoptes-organization / panoptes
  Monitor computational workflows in real time
  ☆73Updated last year
• theislab / batchglm
  Fit generalized linear models in python.
  ☆27Updated 2 years ago
• BD2KGenomics / toil-scripts
  Toil workflows for common genomic pipelines
  ☆33Updated 5 years ago
• chanzuckerberg / ExpressionMatrix2
  Software for exploration of gene expression data from single-cell RNA sequencing.
  ☆28Updated 5 years ago
• lgautier / fastq-and-furious
  Efficient handling of FASTQ files from Python
  ☆51Updated last week
• loosolab / UROPA
  Universal RObust Peak Annotator
  ☆16Updated last year
• mdshw5 / simplesam
  Simple pure Python SAM parser and objects for working with SAM records
  ☆64Updated 2 years ago
• brentp / fishers_exact_test
  Fishers Exact Test for Python (Cython)
  ☆65Updated 2 months ago
• pepkit / looper
  A job submitter for Portable Encapsulated Projects
  ☆22Updated 3 months ago
• KenLauLab / dropkick
  Automated cell filtering for single-cell RNA sequencing data
  ☆24Updated last year
• billgreenwald / pgltools
  Paired Genomic Loci Tool Suite
  ☆30Updated 2 years ago
• schlegelp / catheat
  Plot categorical heatmaps with seaborn
  ☆18Updated 2 years ago
• snakemake-workflows / cookiecutter-snakemake-workflow
  A cookiecutter template for Snakemake workflows
  ☆59Updated 3 years ago
• asrhou / scMatch
  scMatch: a single-cell gene expression profile annotation tool using reference datasets
  ☆24Updated 3 years ago
• bioturing / hera-t
  Hera-T, a fast and accurate tool for estimating gene abundances in single cell data generated by the 10X-Chromium protocol
  ☆17Updated 3 years ago
• afrendeiro / toolkit
  A toolkit for NGS analysis with Python
  ☆14Updated 2 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 5 years ago
• Guannan-Wang / GOMCL
  GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions
  ☆21Updated last year
• seqcode / miniMDS
  ☆29Updated 11 months ago
• dnanexus / wdlTools
  WDL tools for parsing, type-checking, and more
  ☆25Updated last month
• BD2KGenomics / toil-rnaseq
  UC Santa Cruz Computational Genomics Lab's Toil-based RNA-seq pipeline
  ☆41Updated 4 years ago
• broadinstitute / genepy
  Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python
  ☆21Updated 2 years ago
• hawkjo / SDRranger
  ☆10Updated 4 months ago
• dputhier / pygtftk
  A python package and a set of shell commands to handle GTF files
  ☆48Updated 11 months ago
• ncbi / pm4ngs
  Project Manager for NGS data analysis
  ☆31Updated 2 years ago
• higlass / clodius
  Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.
  ☆39Updated last month
• christacaggiano / cell-free-dna-reading-list
  Important papers relating to the biology of cell free DNA
  ☆19Updated 6 years ago