rgranit

supercells

Easily assess quality control data across multiple single cell datasets

scGPT

scanpy

Single-cell analysis in Python. Scales to >1M cells.

decipher

A single-cell analysis toolkit to jointly analyze samples from distinct conditions

cptac

Python packaging for CPTAC data

cellhint

A tool for semi-automatic cell type harmonization and integration

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

scprep

A collection of scripts and tools for loading, processing, and handling single cell data.

seurat-disk

Interfaces for HDF5-based Single Cell File Formats

ML-For-Beginners

12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all

DiffSplice

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

shannonca

Information-based dimensionality reduction

scvelo

RNA Velocity generalized through dynamical modeling

dna-barcodes

Generate robust DNA barcode sets

docstring

Provides docstring like functionality to R functions without requiring the need to create a package.

cellphonedb

examples

A set of examples around pytorch in Vision, Text, Reinforcement Learning, etc.

MeSHHeading2vec

MeSHHeading2vec: A new method for representing MeSH headings as vectors based on graph embedding algorithm

demultiplex

Versatile FASTA/FASTQ demultiplexer.

demo-self-driving

Streamlit app demonstrating an image browser for the Udacity self-driving-car dataset with realtime object detection using YOLO.

tqdm

:zap: A Fast, Extensible Progress Bar for Python and CLI

MultiQC

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

COVID

COVID-19 visualization and analysis

infercnv

Inferring CNV from Single-Cell RNA-Seq

spaCy

💫 Industrial-strength Natural Language Processing (NLP) in Python

biobert

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

vue-tagsinput

A simple tags input with typeahead (autocomplete) built with Vue.js 2.

qupath

QuPath - Bioimage analysis & digital pathology