chris-rands Goto Github PK

anndata

My fork of Annotated data.

annotated_profile_hmms

Sets of protein familes represented as profile HMMs annotated for antibiotic resistance and virulence function.

biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

biopython

My fork of the BioPython repo where I test custom branches (which I delete if they are merged)

biopython-coronavirus

Biopython Jupyter Notebook tutorial to characterize a small genome

biopython-notebook

Notebooks to introduce biopython

biopython.github.io

Source of biopython.org website, migrated from MediaWiki

biopython_workshop

A basic introduction to Biopython, intended for a classroom based workshop

black

The uncompromising Python code formatter

cpython

My fork of the Python programming language

crutils

Various (mostly bioinformatic) utility scripts

emojify

Obfuscate your python script by converting it to emoji icons

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

mmprofiler

Create mmseq2 profiles from (unaligned) protein families/clusters, under development

mmseqs2

My fork of the MMseqs2 repo

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

numpy

The fundamental package for scientific computing with Python.

phagecrannotate

phigaro

My fork of phigaro for bug fixes etc.

public_scrnaseq

[WORK IN PROGRESS] scRNA-seq basic data processing of the genes vs. cells matrix (mirror from gitlab)

rgi

My fork of the Resistance Gene Identifier (RGI).

scanpy

My fork of the scanpy repo

scrublet

Detect doublets in single-cell RNA-seq data

too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.