mckellardw Goto Github PK

anndata

Annotated multivariate observation data in R

awesome_spatial_omics

tools and notes for spatial omics

basecall_snake

Snakemake workflow to run basecalling on ONT data

dnamic

draw_rna

Draw RNA secondary structures in python.

dwm_utils

Tools, wrappers, utilities, and resources for handling single-cell and spatial transcriptomics data

gget

🧬 gget enables efficient querying of genomic reference databases

mckellardw.github.io

David's personal website

minipath

qcbc

ref_snake

Snakemake workflow to automatically build and organize reference genomes for common alignment tasks

scmuscle

The Cornell Single-Cell Muscle Project (scMuscle) aims to collect, analyze and provide to the research community skeletal muscle transcriptomic data

scmuscle2

Curation and analysis of skeletal muscle single-cell data across species

seutils

Utility functions for Seurat

single-cell-vocabulary

slide_snake

Snakemake workflow for the preprocessing, alignment, QC, and quantification of spatial transcriptomics data

spacemake

strs

Suite of analysis tools for spatial total RNA-sequencing

tar-scrna-seq

scRNA-seq analysis beyond gene annotations using transcriptionally active regions (TARs) generated from sequence alignment data

ted

a fully Bayesian approach to deconvolve tumor microenvironment

txg_snake

Snakemake workflow for the alignment, QC, and quantification of all types of 10x Genomics data

utar_lite

Lightweight version of the TAR-scRNA-seq pipeline, redesigned to be barebones and more flexible

vdnamic

Volumetric DNA microscopy

wf-single-cell