noamteyssier

gia

gia: Genomic Interval Arithmetic

bedrs

bedtools-like functionality for interval sets in rust

ggetrs

Efficient querying of biological databases

sgcount

A flexible and fast sgRNA counter from FASTQ Files

crispr_screen

Efficient Differential Expression and Gene Aggregation for CRISPR screens.

alpha-rra

an implementation of αRRA for aggregating grouped p-values

fxtools

a collection of CLI utilities for processing fasta/fastq (FASTX) files.

geomux

hypergeometric testing of guide RNA identity to assign cell barcodes to a guide identity

gtftools

a parser for gtf built using nom

pvsvg

a python wrapper of the vis.js network visualization library with an additional ability to export static SVG

screenviz

crispr screen visualization toolkit

10x_whitelist_mirror

A mirror of the 10X whitelists

10x_cropseq_nextflow

a nextflow pipeline for 10X sequencing CROPSeq

adjustp

A crate to handle various p-value adjustments

bitnuc

A library for efficient nucleotide sequence manipulation using 2-bit encoding

bootstrap_analysis_invivo_crispr_screen

an analysis for estimating the stability of hits and how many mice are required to recover those hits

coitrees

A very fast interval tree data structure

disambiseq

Create unambiguous one-off mismatch libraries for DNA sequences

fxread

a fastx reader

geopagg

geometric p-value aggregation for gene-groups

getset

Getters and Setters for Rust.

howdoi

a collection of technical tutorials

intc

an implementation of the *-INC method to calculate an empirical FDR for non-targeting controls in CRISPR screens

interval_benchmark

Benchmarking suite for gia, bedtools, and bedops

muxsim

a python module for generate cell / guide matrices for demultiplex testing

noamteyssier

repolog

a simple cli utility to annotate and export the contents of a project

scanpy

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

uv

An extremely fast Python package and project manager, written in Rust.

zellij

A terminal workspace with batteries included