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jupyter-perl

Jupyter notebook with IPerl

jupyterlab-slurm

km2gcn

Optimization process of WGCNA hierarchical clustering with k-means

libpyplink

The basic Python API for pgenlib provided by PLINK, split off into its own module

liqa

Long-read Isoform Quantification and Analysis

maestro

Single-cell Transcriptome and Regulome Analysis Pipeline

maglev_switch_mx

manifold_clustering_reduction

mariner

Web interface for controlling MSLA 3D Printers based on Chitu controllers, such as the ones by Elegoo and Phrozen.

markdown-it

Markdown parser, done right. 100% CommonMark support, extensions, syntax plugins & high speed

masc

MASC: Mixed-effects Association testing for Single Cells

matchannot

Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.

merrycrispr

application for designing custom CRISPR libraries.

methylseq

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

milotools

A collection of utility functions compiled here so that I don't have to keep defining them in Jupyter notebooks

modulescorer

Assign scores to gene expression networks.

multi-plier

An unsupervised transfer learning approach for rare disease transcriptomics

multicore-opt-sne

Parallel opt-SNE implementation with Python wrapper

nf-isoseq

Nexflow pipeline for processing PacBio isoseq data

nf-rnaseq

Nextflow pipeline to handle processing of raw RNAseq reads

omicsplayground

Visual analytics platform for multi-omics data.

parallelcluster

Attempting to parallelize portions of the cluster library

phenograph

Subpopulation detection in high-dimensional single-cell data

plier

Pathway-Level Information Extractor (PLIER): a generative model for gene expression data

plinkliftover

Perform liftover on plink files

posterdown

Use RMarkdown to generate PDF Conference Posters via HTML

presentations

Collection of presentations for advanced Python topics

pygmst

Python translation of GeneMarkS-T

pyhsiclasso

Versatile Nonlinear Feature Selection Algorithm for High-dimensional Data

pyplier

Python translation of PLIER