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adasampling

Package for positive unlabeled and label noise learning

bioinfosummer2015

cepo

Uncovering cell identity genes using differential stability of expression in single cells.

cluer

Cluster Evaluation R package (ClueR) for detecting key signaling events from time-series phosphoproteomics data

deepmerge

devtools

Tools to make an R developer's life easier

directpa

A package for pathway analysis in experiments with multiple perturbation designs.

dplyr

Plyr specialised for data frames: faster & with remote datastores

esc-multiome

Multi-omic profiling reveals dynamics of the phased progression of pluripotency

geneticensemble

imbalanced-data-sampling

Automatically exported from code.google.com/p/imbalanced-data-sampling

imbalanced-data-sampling.image

Automatically exported from code.google.com/p/imbalanced-data-sampling.image

ksp-puel

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data

matilda

Matilda is a multi-task framework for learning from single-cell multimodal omics data. Matilda leverages the information from the multi-modality of such data and trains a neural network model to simultaneously learn multiple tasks including data simulation, dimension reduction, visualization, classification, and feature selection.

pad

PAD (Proximal and Distal) clustering

phosr

PhosR is a package for the comprehensive analysis of phosphoproteomic data.

phosr_star_protocols

pyanglab.github.io

Pengyi Yang Lab

refraction

A supervised machine learning approach for deterministic identification of MS-based proteome

rstan

RStan, the R interface to Stan

sample_subset_optimization

scccess

Single-cell Consensus Clusters of Encoded Subspaces

scdeepfeatures

Deep learning-based feature selection for single-cell omics data

scmultibench

Multi-task benchmarking of single-cell multimodal omics integration methods

scnet

R package with collection of single cell RNA-sequencing (scRNA-seq) data analysis functions

segs

Identify stably expressed genes from single-cell RNA-seq data

self-boosted-percolator

Automatically exported from code.google.com/p/self-boosted-percolator

snapccess

Ensemble deep learning of embeddings for clustering multimodal single-cell omics data

snapkin

spss