PYangLab

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.

PhosR

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

scCCESS

Single-cell Consensus Clusters of Encoded Subspaces

AdaSampling

Package for positive unlabeled and label noise learning

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

KSP-PUEL

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

scDeepFeatures

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

SnapCCESS

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

SEGs

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

SVGbench

Evaluating spatially variable gene detection methods for spatial transcriptomics data

scMultiBench

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

DeepMerge

PhosR_STAR_Protocols

SnapKin

TransOmicsData

A collection of trans-omic datasets

BioInfoSummer2015

ESC-multiome

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

directPA

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

dplyr

Plyr specialised for data frames: faster & with remote datastores

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

PAD

PAD (Proximal and Distal) clustering

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

scNet

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

self-boosted-percolator

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

SPSs