mckellardw

DWM_utils

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

mckellardw.github.io

David's personal website

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

slide_snake

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

STRS

Suite of analysis tools for spatial total RNA-sequencing

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

mckellardw/scMuscle

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

mckellardw/STRS

Suite of analysis tools for spatial total RNA-sequencing

mckellardw/slide_snake

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

mckellardw/ref_snake

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

mckellardw/scMuscle2

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

mckellardw/seutils

Utility functions for Seurat

mckellardw/DWM_utils

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

mckellardw/mckellardw.github.io

David's personal website

mckellardw/txg_snake

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

mckellardw/anndata

Annotated multivariate observation data in R

mckellardw/basecall_snake

Snakemake workflow to run basecalling on ONT data

mckellardw/uTAR_lite

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

mckellardw/awesome_spatial_omics

tools and notes for spatial omics

mckellardw/bioRxiv-word-template

MS Word template for styling a manuscript for a bioRxiv submission

mckellardw/dnamic

mckellardw/draw_rna

Draw RNA secondary structures in python.

mckellardw/gget

🧬 gget enables efficient querying of genomic reference databases

mckellardw/minipath

mckellardw/qcbc

mckellardw/runon_snake

Lightweight snakemake pipeline for preprocessing, alignmen, and QC of PROseq/ChROseq data

mckellardw/single-cell-vocabulary

mckellardw/spacemake

mckellardw/TAR-scRNA-seq

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

mckellardw/TED

a fully Bayesian approach to deconvolve tumor microenvironment

mckellardw/vdnamic

Volumetric DNA microscopy

mckellardw/wf-single-cell