Chan Zuckerberg Biohub

Repositories

• iggtools

  Microbiome - Integrated Gut Genome
  Python MIT 1 3 6 7 Updated May 13, 2020

• sc2-msspe-bioinfo

  bioinformatics for sars-cov-2 msspe protocol

  bioinformatics pipeline nextflow covid-19 covid19 covid19-sequencing msspe
  Nextflow 2 0 8 2 Updated May 13, 2020

• luminoth-uv-imaging

  Forked from tryolabs/luminoth

  Object detection using Faster RCNN, SSD
  Python BSD-3-Clause 400 1 0 0 Updated May 13, 2020

• molecular-cross-validation

  Calibrate and compare methods for denoising single-cell RNA-seq data
  Python MIT 1 16 0 0 Updated May 13, 2020

• sourmash

  Forked from dib-lab/sourmash

  Compute and compare MinHash signatures for DNA data sets.
  Python 37 3 0 1 Updated May 12, 2020

• EpiGen-COVID19

  Using both phylogenetic and time-series data from the COVID19 pandemic to estimate number of missing infections and predict forward epidemic trajectory.
  R 0 0 0 0 Updated May 12, 2020

• nf-predictorthologs

  *de novo* orthologous gene predictions from bam + bed or fasta/fastq data
  Nextflow MIT 1 2 16 (1 issue needs help) 2 Updated May 12, 2020

• sencha

  Sencha is a Python package for directly translating RNA-seq reads into coding protein sequence.
  Python MIT 1 4 17 (1 issue needs help) 4 Updated May 12, 2020

• ninjaMap

  [BETA] Abundance estimator at strain level resolution for microbial communities.
  Python 0 0 0 0 Updated May 11, 2020

• de-novo-orthology-paper

  Manuscript for functional prediction of transcriptomic “dark matter” across species
  HTML 3 10 23 1 Updated May 11, 2020

• cerebra

  high-throughput summarizing of vcf entries following a sequencing experiment

  mutations cancer-genomics scrna-seq variant-calling
  Jupyter Notebook MIT 3 20 8 0 Updated May 11, 2020

• scRFE
  Jupyter Notebook MIT 1 2 0 0 Updated May 9, 2020

• BioE-COVID19

  Software for hardware systems built in response to emerging needs
  C++ MIT 0 0 0 0 Updated May 9, 2020

• pysero

  serological measurements from multiplexed ELISA assays

  python imaging elisa covid-19 covid19 covid19-serology antigen-arrays
  Jupyter Notebook MIT 1 2 14 2 Updated May 9, 2020

• test-datasets

  Forked from nf-core/test-datasets

  Test data to be used for automated testing with the nf-core pipelines
  MIT 57 0 0 3 Updated May 9, 2020

• setup-pyproject

  A GitHub action for initializing a Python project and caching dependencies
  TypeScript MIT 0 0 0 0 Updated May 8, 2020

• seqbot

  Scripts for sequencing automation
  Python MIT 1 0 0 0 Updated May 8, 2020

• dotblotr

  dotblotr: a microarray image processing package
  Python MIT 0 0 0 0 Updated May 7, 2020

• auspice

  Forked from nextstrain/auspice

  Web app for visualizing pathogen evolution
  JavaScript AGPL-3.0 112 0 0 0 Updated May 7, 2020

• crispycrunch

  Web app for CRISPR experiment setup and analysis

  postgres django crispr fastq-files biohub
  Python MIT 1 3 0 0 Updated May 6, 2020

• pyxi

  xi correlation method adapted for python
  Jupyter Notebook 0 0 0 0 Updated May 5, 2020

• darmanis_group_DL_notebook

  Misc work for biohub projects
  Jupyter Notebook MIT 0 1 0 0 Updated May 5, 2020

• kh-workflows

  Nextflow workflow commands for kmer hashing
  Shell MIT 0 1 0 5 Updated May 3, 2020

• insta_paper
  MIT 0 0 2 1 Updated May 3, 2020

• configs

  Forked from nf-core/configs

  Config files used to define parameters specific to compute environments at different Institutions.
  Nextflow MIT 35 0 0 0 Updated May 3, 2020

• microbiome-data-analysis

  Contains docker images and scripts to perform upstream bioinformatic analysis for CZ Biohub Microbiome Initiative samples.
  Python 0 1 0 0 Updated May 1, 2020

• ProteinPurifier

  Contains Python application and czpurifier package for automated protein purification
  Python MIT 0 1 0 0 Updated May 1, 2020

• al-mosquito-id

  mosquito identification using DL
  Jupyter Notebook 0 0 0 0 Updated Apr 30, 2020

• 2020-ncbi-genomes

  Analyze metadata of genomes submitted to NCBI
  MIT 0 0 0 0 Updated Apr 30, 2020

• bam2fasta

  Package to convert bam files to fasta per single cell barcode
  Python MIT 1 4 6 0 Updated Apr 29, 2020