Prete's repositories
anndata
Annotated data.
atacseq
ATAC-seq peak-calling, QC and differential analysis pipeline
bioconda-recipes
Conda recipes for the bioconda channel.
bsub_jupyter_lab
start jupyterlab python and R server on LSF farm5 node via bsub
cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
celltypist_wiki
Materials and scripts for building cell type encyclopedia table
cellxgene
An interactive explorer for single-cell transcriptomics data
configs
Config files used to define parameters specific to compute environments at different Institutions
fastq_utils
Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
geosketch
Geometry-preserving random sampling
hello
Classic hello world script in Nextflow language
jupyter-remote-desktop-proxy
Run a Linux Desktop on a JupyterHub
jupyterhub-the-hard-way
Understanding JupyterHub by deploying it step by step
librdata
Read and write R data frames from C
nextflow
A DSL for data-driven computational pipelines
sceasy
A package to help convert different single-cell data formats to each other
science-gateway
Unidata Science Gateway
spacexr
Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics
ULTRA
ULTRA Locates Tandemly Repetitive Areas