audit_item_status

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

External Lab, Community

metasvm

MetaSVM

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

Mark Craven, UW Madison

esm-1v-workflow

ESM-1v variant scoring workflow

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

varity

VARITY

cellspace

CellSpace

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

scanpy

Scanpy

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

Martin Kircher, BIH

cadd

CADD

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

Tim Reddy, Duke

reddy-starrseq-read-processing

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

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

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

MAGeCK

Jesse Engreitz, Stanford

Luca Pinello, MGH

crispr-surf

CRISPR-SURF

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

bowtie2

Bowtie 2

Predrag Radivojac, Northeastern

mutpred-lof

MutPred-LOF

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

pairtools

Singel Cell ATAC-seq (scATAC) analysis and clustering

snapatac2

snapATAC2

Alan Boyle, UMich

surf and turf

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

REVEL

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

aloft

ALoFT

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

Lars Steinmetz, Stanford

tapseq-r-package

TAPseq (R package)

A quality control tool for high throughput sequence data.

fastqc

FastQC

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

Lior Pachter, Caltech

lsrrsrlfkotwmwmp-2024

Repository for reproducing results for lr-kallisto

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

splitcode

NumPy is a software enabling numerical computing with Python.

numpy

NumPy

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

Lab

Award

Status