letaylor

docker-letaylor

marker_gene_db

This repository contains lists of various marker genes.

variantBedOverlap

Calculates the overlap of variants in LD with features from BED files

batchbench

cellBrowser

Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org

CELLECT

CELLECT (CELL-type Expression-specific integration for Complex Traits)

CELLEX

CELLEX (CELL-type EXpression-specificity)

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

chemprop

Message Passing Neural Networks for Molecule Property Prediction

conda-letaylor

Conda recipes

DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.

docker-letaylor-travis

Docker images

drawCell

R package to create cell pictures.

dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow

gwas-lecture

Lectures on Genome Wide Association Studies (GWAS) using Python, Limix and Jupyter Noteboos

harmony-pytorch

MPRA_Khetan

muon

muon is a multimodal omics Python framework

nfCore_scRNA

Combined Repo of the Cellbender, Deconvolution and QC metrics placed in nfCore template for transferability between institutions and different HPC setups.

performance

:muscle: Models' quality and performance metrics (R2, ICC, LOO, AIC, BF, ...)

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

scanpy_usage

Scanpy use cases.

scfind

ScreenProcessing

scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

scrublet

A repository for the scrublet module of the vib-singlecell-nf pipeline

skylab

Secondary analysis pipelines

spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

TwoSampleMR

R package for performing 2-sample MR using MR-Base database

zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs