adler-sudo

vim-python-pep8-indent

A nicer Python indentation style for vim.

unidex

python implementation of a universal demultiplexer built in mind for combinatorial indexing

excluderanges

Genomic coordinates of problematic genomic regions as GRanges

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

TED

a fully Bayesian approach to deconvolve tumor microenvironment

loguru

Python logging made (stupidly) simple

scipy

SciPy library main repository

scikit-learn

scikit-learn: machine learning in Python

oneliners

Useful bash one-liners for bioinformatics.

CITEViz

CITEViz: Replicating the Interactive Flow Cytometry Workflow in CITE-Seq

parallel-fastq-dump

parallel fastq-dump wrapper

ncomms-20-10056-t

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

atac-seq-analysis

Visualize scATAC-seq profiles using PCA and UMAP. Construct a support vector classifier (SVC) to predict cell type given ATAC-seq expression profile.

Deduper-adler-sudo

deseq

Demultiplex

motif-mark

Generate image of genes given fasta file and motif file. The image identifies exons, introns, and locations of motifs within the gene.

QAA

scaden

Deep Learning based cell composition analysis with Scaden.

scGAN

Realistic in silico generation and augmentation of single cell RNA-seq data using Generative Adversarial Neural Networks

grip

Graph Integration Platform

scico

Palettes for R based on the Scientific Colour-Maps

AgingClock

Demultiplex

Tool to Demultiplex and determine the level of index swapping and undetermined index-pairs, before and after quality filtering of index reads.

MARVEL

The MARVEL assembler

automl

Google Brain AutoML

microblog

The microblogging application developed in my Flask Mega-Tutorial series. This version maps to the 2024 Edition of the tutorial.

smartPot