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quantile_normalize

This function implements quantile normalization in python matrix

r2u

CRAN as Ubuntu Binaries

raceid

Algorithm for the inference of cell types from single-cell RNA-seq data.

raceid3_stemid2

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. Please download the R package from the RaceID3_StemID2_package repository, which contains the current version as an R package. This repository will not be updated anymore.

raceid3_stemid2_package

Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and StemID2 method including novel functionalities and performance improvements compared to the previous RaceID3/StemID2 version in the RaceID3_StemID2 repository. The RaceID3_StemID2 repository will not be updated anymore in the future.

random-forest

Implementation of a Random Forest classifier in both Python and Scala

random-forest-classifier

A very simple Random Forest Classifier implementation in python.

random-forest-classifier-1

A random forest classifier written in python.

rfunctions

a set of R functions that I find useful

rjmcmc

RJMCMC

rnaseqgene

RNA-seq workflow: gene-level exploratory analysis and differential expression

rtsne

An R package for t-SNE (t-Distributed Stochastic Neighbor Embedding)

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

sameclustering

SAME (Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble): Cluster ensemble for single-cell RNA-seq data

sartools

Statistical Analysis of RNA-Seq Tools

sc-type

scabc

scanalysis

Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

scatac-seq_notes

scATAC-seq data analysis tools and papers

sccatch

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

sccatch_performance_comparison

The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database

sccoda

A Bayesian model for compositional single-cell data analysis

scde

R package for analyzing single-cell RNA-seq data

schcl

scikit-learn

scikit-learn: machine learning in Python

scina

SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples

scmiko

R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.

scope

Fast visualization tool for large-scale and high dimensional single-cell data

scpipeline

Single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports

scrat