letaylor
Geneticist at Wellcome Sanger Institute and NIH/NHRI. Previously at Calico, EMBL-EBI, and University of Cambridge.
Pinned Repositories
binder-demo-share_results
Demo for sharing results (e.g., a csv file) using qgrid, Binder, and Jupyter.
docker-letaylor
limix_cl
Command tool for LIMIX.
marker_gene_db
This repository contains lists of various marker genes.
reference_1000G
Process 1000G phase3 data as a reference for various populations.
snakemake-qtl
Snakemake pipeline for molecular trait QTL mapping
variantBedOverlap
Calculates the overlap of variants in LD with features from BED files
letaylor's Repositories
letaylor/docker-letaylor
letaylor/marker_gene_db
This repository contains lists of various marker genes.
letaylor/variantBedOverlap
Calculates the overlap of variants in LD with features from BED files
letaylor/batchbench
letaylor/cellBrowser
Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
letaylor/CELLECT
CELLECT (CELL-type Expression-specific integration for Complex Traits)
letaylor/CELLEX
CELLEX (CELL-type EXpression-specificity)
letaylor/cellpose
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
letaylor/chemprop
Message Passing Neural Networks for Molecule Property Prediction
letaylor/conda-letaylor
Conda recipes
letaylor/DENTIST
DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.
letaylor/docker-letaylor-travis
Docker images
letaylor/drawCell
R package to create cell pictures.
letaylor/dropSeqPipe
A SingleCell RNASeq pre-processing snakemake workflow
letaylor/gwas-lecture
Lectures on Genome Wide Association Studies (GWAS) using Python, Limix and Jupyter Noteboos
letaylor/harmony-pytorch
letaylor/MPRA_Khetan
letaylor/muon
muon is a multimodal omics Python framework
letaylor/nfCore_scRNA
Combined Repo of the Cellbender, Deconvolution and QC metrics placed in nfCore template for transferability between institutions and different HPC setups.
letaylor/performance
:muscle: Models' quality and performance metrics (R2, ICC, LOO, AIC, BF, ...)
letaylor/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
letaylor/scanpy_usage
Scanpy use cases.
letaylor/scfind
letaylor/ScreenProcessing
letaylor/scRNAseq-analysis-notes
scRNAseq analysis notes from Ming Tang
letaylor/scrublet
A repository for the scrublet module of the vib-singlecell-nf pipeline
letaylor/skylab
Secondary analysis pipelines
letaylor/spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
letaylor/TwoSampleMR
R package for performing 2-sample MR using MR-Base database
letaylor/zUMIs
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs