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ampad-diffexp

Code base for performing covariate adjustments and differential expression analysis of the RNAseq data from AMP-AD.

aucell

AUCell: score single cells with gene regulatory networks

beds

Bagging Ensemble Deep Segmentation for Nucleus Segmentation with Testing Stage Stain Augmentation

bhtsne

Barnes-Hut t-SNE

biogpt

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellphonedb

combat-seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

consensus_clustering

An implementation of Consensus clustering in Python

coursescheduler

A web interface to help student register account and select courses.

deeplab-v3

Google DeepLab V3 for Image Semantic Segmentation

deeppath

Classification of Lung cancer slide images using deep-learning

deseq2

Differential gene expression analysis based on the negative binomial distribution

dicer

Diverse Cluster Ensemble in R

digit-path

emr_nlp_machinelearning

A project to process free-text clinical reports with NLP and machine learning

eqtl-catalogue-resources

fastqtl

Enhanced version of the FastQTL QTL mapper

fingerprint_maps

Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.

gate

genetic-algorithm-and-machine-learing

The objective of this study is to develop a GA-based approach, utilizing a feedback linkage between feature selection and classification.

gglocuszoom

Create LocusZoom-style plots in R.

gtexresults

Code and data resources accompanying Urbut et al (2017), "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions."

he2rna_code

Train a model to predict gene expression from histology slides.

hover_net

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.

ibdtherapyresponsepaper

Analyses and code associated with https://doi.org/10.1038/s41591-021-01520-5

liger

R package for integrating and analyzing multiple single-cell datasets

lme4qtl

Mixed models @lme4 + custom covariances + parameter constraints

mashr

An R package for multivariate adaptive shrinkage.

metacells

Metacells - Single-cell RNA Sequencing Analysis