Tyrev

seurat

R toolkit for single cell genomics

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

abagen

A toolbox for working with Allen Human Brain Atlas microarray expression data

Single-nuclei-epigenomic-and-transcriptomic-landscape-in-Alzheimer-disease

Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease

cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

alevinQC

Create QC and summary reports for Alevin output

R2SN_construction

BrainRadiomicsTools

A radiomics tool with a variety of brain MRI processing functions, including affine registration, hippocampus segmentation and feature calculation.

allenBrain

:mouse: Acquiring images from allen brain atlas, mouse ISH experiments in R.

BRAPH

Brain Analysis using Graph Theory

Vini

The Vini in silico model of cancer

dreamlet

Perform differential expression analysis on cohort-scale single cell datasets using linear mixed models

ilincsAPI

MegaGO

Calculate semantic distance for sets of Gene Ontology terms

MIST

pymbn

OntoApps-Stanford

An umbrella platform for all my Biomedical Web applications

TREA

Transcriptional Regulator Enrichment Analysis

FunkyTax

An R package for characterizing taxonomic and functional relationships among microbiome communities.

LSLODQuery

Set of scripts to analyze the LSLOD Cloud