Noam Teyssier

gia. gia: Genomic Interval Arithmetic

bedrs. bedtools-like functionality for interval sets in rust

paraseq. A minimal copy fastq and fasta reader built for parallel support and paired end processing

ggetrs. Efficient querying of biological databases

adpbulk. pseudobulking on an AnnData object

ibu. a rust library for high throughput binary encoding of genomic sequences

sgcount. A flexible and fast sgRNA counter from FASTQ Files

crispr_screen. Efficient Differential Expression and Gene Aggregation for CRISPR screens.

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

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

seq_io_parallel. a map-reduce parallel processing extension for seq_io

idea. Integrated Differential Expression and Annotation

nucgen. A fast and simple configurable fast[aq] generator

seqpls. "My sequences please" - a paired fastq grepper

graph-canon. Generate canonical labels for graphs built on NAUTY

qgpu. A simple job scheduler across multi-node gpus

pipspeak. a CLI tool to whitelist filter pipseq reads and convert them to a 10X-style format

screenviz. crispr screen visualization toolkit

memoesu. subgraph enumeration on graphs using a memoized parallel ESU algorithm

splici. a rust implementation of the splici algorithm to build spliced/unspliced transcripts

yaflux. A lightweight, declarative framework for Python analysis workflows.

gtftools. a parser for gtf built using nom

cshift. A tool to perform cluster enrichment/depletion analyses

alpha-rra. an implementation of αRRA for aggregating grouped p-values

graph6-rs. a rust library for graph6 formatted files from NAUTY

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

dgcount. Dual guide CRISPR counting

casmap. Mapping sgRNA counts for cas12 6-mer CRISPR screens

graphtries. a rust implementation of the gtries subgraph enumeration algorithm

dirio. a simple CLI to track and report disk usage over some subcommand runtime

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

information. ndarray-based information theory utilities

bitnuc-mismatch. Create unambiguous one-off mismatch hash tables from bitnuc scalars

art_or_trash. is it art? or is it trash?

gtfjson. A simple CLI utility to convert a GTF file to NDJSON for fast parsing

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

ClusterDock. Pipeline and analysis scripts for k-mean based clustering of DOCK