noamteyssier

Bioinformatics at the intersection of systems biology, machine learning, and functional genomics in neurodegenerative disease

UCSFSan Francisco, California

Pinned Repositories

adpbulk
pseudobulking on an AnnData object
Language:Python24 2 71
bedrs
bedtools-like functionality for interval sets in rust
Language:Rust34 1 801
crispr_screen
Efficient Differential Expression and Gene Aggregation for CRISPR screens.
Language:Rust6 1 900
geomux
hypergeometric testing of guide RNA identity to assign cell barcodes to a guide identity
Language:Python1 1 221
ggetrs
Efficient querying of biological databases
Language:Rust28 2 1142
gia
gia: Genomic Interval Arithmetic
Language:Rust51 1 672
idea
Integrated Differential Expression and Annotation
Language:HTML4 1 150
pipspeak
a CLI tool to whitelist filter pipseq reads and convert them to a 10X-style format
Language:Rust4 1 83
qgpu
A simple job scheduler across multi-node gpus
Language:Rust5 1 91
sgcount
A flexible and fast sgRNA counter from FASTQ Files
Language:Rust8 2 410

noamteyssier's Repositories

noamteyssier/gia
gia: Genomic Interval Arithmetic
Language:Rust51 1 672
noamteyssier/bedrs
bedtools-like functionality for interval sets in rust
Language:Rust34 1 801
noamteyssier/ggetrs
Efficient querying of biological databases
Language:Rust28 2 1142
noamteyssier/sgcount
A flexible and fast sgRNA counter from FASTQ Files
Language:Rust8 2 410
noamteyssier/crispr_screen
Efficient Differential Expression and Gene Aggregation for CRISPR screens.
Language:Rust6 1 900
noamteyssier/idea
Integrated Differential Expression and Annotation
Language:HTML4 1 150
noamteyssier/pipspeak
a CLI tool to whitelist filter pipseq reads and convert them to a 10X-style format
Language:Rust4 1 83
noamteyssier/alpha-rra
an implementation of αRRA for aggregating grouped p-values
Language:Rust20
noamteyssier/casmap
Mapping sgRNA counts for cas12 6-mer CRISPR screens
Language:Rust2 1 31
noamteyssier/fxtools
a collection of CLI utilities for processing fasta/fastq (FASTX) files.
Language:Rust2 1 391
noamteyssier/geomux
hypergeometric testing of guide RNA identity to assign cell barcodes to a guide identity
Language:Python1 1 221
noamteyssier/gtftools
a parser for gtf built using nom
Language:Rust1 1 60
noamteyssier/pvsvg
a python wrapper of the vis.js network visualization library with an additional ability to export static SVG
Language:JavaScript1 1 41
noamteyssier/screenviz
crispr screen visualization toolkit
Language:Python1 1 7
noamteyssier/10x_whitelist_mirror
A mirror of the 10X whitelists
0 1 00
noamteyssier/adjustp
A crate to handle various p-value adjustments
Language:Rust1 7
noamteyssier/bootstrap_analysis_invivo_crispr_screen
an analysis for estimating the stability of hits and how many mice are required to recover those hits
Language:Jupyter Notebook
noamteyssier/coitrees
A very fast interval tree data structure
Language:Rust
noamteyssier/disambiseq
Create unambiguous one-off mismatch libraries for DNA sequences
Language:Rust
noamteyssier/fxread
a fastx reader
Language:Rust1 191
noamteyssier/geopagg
geometric p-value aggregation for gene-groups
Language:Rust
noamteyssier/getset
Getters and Setters for Rust.
Language:Rust0 0
noamteyssier/gia_benchmark
a benchmark of gia and bedtools on various functionality
Language:Jupyter Notebook1 0
noamteyssier/howdoi
a collection of technical tutorials
Language:JavaScript1 5
noamteyssier/intc
an implementation of the *-INC method to calculate an empirical FDR for non-targeting controls in CRISPR screens
Language:Rust
noamteyssier/interval_benchmark
Benchmarking suite for gia, bedtools, and bedops
Language:Jupyter Notebook1 0
noamteyssier/pypage
python implementation of the PAGE algorithm
Language:Python0 0
noamteyssier/repolog
a simple cli utility to annotate and export the contents of a project
Language:Rust
noamteyssier/scanpy
Single-cell analysis in Python. Scales to >1M cells.
Language:Python0 0
noamteyssier/zellij
A terminal workspace with batteries included
Language:Rust