zyllifeworld

DEGAS

DEGAS is an R package that can be used to prioritize cells in relation to disease.

scDINO

Self-Supervised Vision Transformers for multiplexed imaging datasets

RAPToR

RAPToR (Real Age Prediction from Transcriptome staging on Reference) is a tool to accurately predict individual samples' developmental age from their gene expression profiles.

SEVtras

sEV-containing droplet identification in scRNA-seq data (SEVtras)

SCALEX

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

GeneNMF

Methods to discover gene programs on single-cell data

genome_assembly_tools

List of genome assembly tools

MuSE

Somatic point mutation caller

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

ImmunoTyper-SR

Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

bioicons

A library of free open source icons for science illustrations in biology and chemistry

2024_Chandrasekaran_NatureMethods

MapSplice

Bioinformatics software release from Jinze Liu's Bioinformatics lab @ UKy

single_cell_classification

Methods to use SNPs or gene expression to classify single cell RNAseq to reference profiles

decoupleR

R package to infer biological activities from omics data using a collection of methods.

TCGAmutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

R6

Encapsulated object-oriented programming for R

CharGer

Characterization of Germline variants

SenCID

Senescent Cell Identification

seqr

web-based analysis tool for rare disease genomics

LINGER

truvari

Structural variant toolkit for VCFs

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

gatk-sv

A structural variation pipeline for short-read sequencing

EpiTrace

Cell age determination by scATAC-seq and bulk-ATAC-seq

spatial-bonemarrow-atlas

This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Proteomic Profiling Reveals the Cellular Composition and Spatial Organization of the Human Bone Marrow Microenvironment"

MM_ABM

Multiple Myeloma Mathematical Model

VisCello

Viscello for Visualization of Single Cell Data

HiNT

HiC for copy Number variation and Translocation detection

PERCEPTION

Utilizing single-cell omics from patients tumor to predict response and resistance.