noamteyssier

Noam Teyssier's repositories

gia

gia: Genomic Interval Arithmetic

Language:RustMIT49 1 66

bedrs

bedtools-like functionality for interval sets in rust

Language:RustMIT31 1 80

ggetrs

Efficient querying of biological databases

Language:RustMIT28 2 112

sgcount

A flexible and fast sgRNA counter from FASTQ Files

Language:Rust8 2 41

crispr_screen

Efficient Differential Expression and Gene Aggregation for CRISPR screens.

Language:Rust600

idea

Integrated Differential Expression and Annotation

Language:HTMLMIT3 1 15

pipspeak

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

Language:RustMIT3 1 8

splici

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

Language:RustMIT3 1 3

casmap

Mapping sgRNA counts for cas12 6-mer CRISPR screens

Language:Rust2 1 3

fxtools

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

Language:RustMIT2 1 36

geomux

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

Language:PythonMIT1 1 22

gtftools

a parser for gtf built using nom

Language:RustMIT100

memoesu

subgraph enumeration on graphs using a memoized parallel ESU algorithm

Language:RustMIT1 1 29

pvsvg

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

Language:JavaScriptMIT1 1 4

screenviz

crispr screen visualization toolkit

Language:PythonMIT1 1 6

10x_rna_velocity_nextflow

A nextflow pipeline for running RNA velocity splice aware mapping on 10x fastqs

Language:NextflowMIT000

adjustp

A crate to handle various p-value adjustments

Language:RustMIT01 6

CZI_NDCN_Webinar_Session1

The results of the workshop and example data from CZI NDCN Webinar Session 1

Language:HTMLMIT000

faiquery

perform interval queries on an indexed fasta file

Language:RustMIT01 1

fxread

a fastx reader

Language:Rust01 19

gia_benchmark

a benchmark of gia and bedtools on various functionality

Language:Jupyter NotebookMIT010

gtfjson

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

Language:RustMIT01 5

gtfparse

Parsing tools for GTF (gene transfer format) files

Language:PythonApache-2.0000

howdoi

a collection of technical tutorials

Language:JavaScriptMIT01 5

interval_benchmark

Benchmarking suite for gia, bedtools, and bedops

Language:Jupyter NotebookMIT000

pypage

python implementation of the PAGE algorithm

Language:PythonMIT000

scanpy

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

Language:PythonBSD-3-Clause000

sciseq_rna_velocity_nextflow

A nextflow pipeline for running RNA velocity splice aware mapping on sciseq fastqs

Language:NextflowMIT000

scispeak

a rust parser to convert sci-rna-seq3 reads into 10x compatible formats

Language:RustMIT000

screen_libraries

Screening libraries used in the Kampmann lab

000