Ensemble-based approaches (support vector machine) that integrates multiple scoring methods.

metasvm

released

MetaSVM

Workflow and supporting code for evaluating every amino acid human protein substitution using ESM-1v.

esm-1v-workflow

released

ESM-1v variant scoring workflow

VARITY is an approach for pathogenicity prediction, which has been specifically optimized for rare missense variation.

varity

released

VARITY

Single Cell Multiome

scATAC batch integration + analysis

cellspace

released

CellSpace

Single Cell Multiome

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata.

scanpy

released

Scanpy

Genome-wide single nucleotide variants and short indels effects/prioritization.

cadd

released

CADD

Reddy lab's scripts for processing FASTQs produced from STARR-seq.

reddy-starrseq-read-processing

released

Reddy lab STARR-seq read processing script

gMVP is a graph attention neural network model designed to effectively represent or learn the representation of protein sequence and structure context to improve missense variant prediction of disease impact.

gmvp

released

gMVP

A high-throughput web-server capable of predicting the functional consequences of both coding variants, i.e. non-synonymous single nucleotide variants (nsSNVs), and non-coding variants in the human genome.

fathmm

released

FATHMM

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.

mageck

released

MAGeCK

Target gene prediction (element)

abc

released

ABC

CRISPR Screens

Design and analyses of tiling screens

crispr-surf

released

CRISPR-SURF

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

bowtie2

released

Bowtie 2

Coding variant effects/prioritization

mutpred-lof

released

MutPred-LOF

pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.

pairtools

released

pairtools

Single Cell Multiome

Singel Cell ATAC-seq (scATAC) analysis and clustering

snapatac2

released

snapATAC2

Noncoding variant effects/prioritization

surf and turf

released

SURF and TURF

REVEL is an ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons.

revel

released

REVEL

ALoFT provides extensive annotations to putative loss-of-function variants (LoF) in protein-coding genes including functional, evolutionary and network features.

aloft

released

ALoFT

CRISPR Screens

Design TAP-seq primers for a set of target genes for targeted scRNA-seq

tapseq-r-package

released

TAPseq (R package)

A quality control tool for high throughput sequence data.

fastqc

released

FastQC

Repository of code associated with "Long-read sequencing transcriptome quantification with lr-kallisto" by Rebekah Loving et al., 2024

lsrrsrlfkotwmwmp-2024

released

Repository for reproducing results for lr-kallisto

splitcode is a tool that enables flexible and efficient parsing, interpreting and editing of sequencing reads.

splitcode

released

splitcode

NumPy is a software enabling numerical computing with Python.

numpy

released

NumPy

PrimateAI is a deep residual neural network for classifying the pathogenicity of missense mutations.

primateai

released

PrimateAI