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immucan-scdb

irap

integrated RNA-seq Analysis Pipeline

isee

R/shiny interface for interactive visualization of data in objects derived from the SummarizedExperiment class

jule.torch

Torch code for our CVPR 2016 paper "Joint Unsupervised LEarning of Deep Representations and Image Clusters"

kallisto

Near-optimal RNA-Seq quantification

keras

Deep Learning for humans

libra

libsvm

loompy

Python implementation of the Loom file format - http://loompy.org

maca

MACA: Marker-based automatic cell-type annotation for single cell expression data

machine-learning

Practical Full-Stack Machine Learning

magic

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

manifold-clustering-algorithm

The source code to cluster multiple manifolds with intersection

microscope

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

mixrf

A random-forest-based approach for imputing clustered incomplete data

mixture-autoencoder

Implementation of "Deep Unsupervised Clustering Using Mixture of Autoencoders"

multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

muon

muon is a multimodal omics Python framework

muscat

Multi-sample multi-group scRNA-seq analysis tools

mycodes

nd

ImageJ plugin for image analysis of porous materials

neural-networks

Python code and data sets used in the post on neural networks.

neural_network_kotlin

Autoencoder + Deep Autoencoder + Deep Convoluted Autoencoder + Hebbian

pagoda2

R package for analyzing and interactively exploring large single-cell RNA-seq datasets

pcreode

An algorithm for mapping cell state transitions.

perl-rna-seq-star

STAR + HTSeq + featureCounts RNA-seq processing pipeline environment and wrapper script, including SRA query, download, and caching functionality and useful reuse/restart features

popsicler

popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.

presto

Fast Wilcoxon and auROC

pyrcc

Python implementation of Robust Continuous Clustering

quantile_normalize

This function implements quantile normalization in python matrix