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sbo

The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.

scanpy-tutorials

Scanpy Tutorials.

scanpy_squidpy_demo_2021

scbert

scbonita

Regulatory rule inference, pathway analysis, and cell signaling analysis with scRNAseq data

scdeal

Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-seq data

scdeepcluster

scDeepCluster for Single Cell RNA-seq data

scelvis

:sparkler: SCelVis - web-based visualization of single-cell data. :arrow_right: :arrow_right: Demo :arrow_right::arrow_right:

scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

scgist

scikit-learn

scikit-learn: machine learning in Python

scikit-learn-videos

Jupyter notebooks from the scikit-learn video series

scimap_phenotyping

Galaxy tool wrappers for single cell phenotyping analysis using Scimap, Squidpy, Vitessce etc.

scipy

SciPy library main repository

scmlnet

Single-cell RNA-seq data-based inference of multilayer inter- and intra-cellular signaling networks

scnym

Semi-supervised adversarial neural networks for classification of single cell transcriptomics data

scpipe

a pipeline for single cell RNA-seq data analysis

scplc

Codes for the scPLC project

scrabble

Single Cell RNA-Seq imputAtion constrained By BuLk RNAsEq data (SCRABBLE)

scrna-seq-data-analysis-achiev

scRNAseq Achieve

scrna-seq_notes

A list of scRNA-seq analysis tools

scrna-seq_online-full-course2

scrna-tools

Table of software for the analysis of single-cell RNA-seq data.

scrna.seq.course

Analysis of single cell RNA-seq data course

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

scrnaseq-analysis-notes

scRNAseq analysis notes from Ming Tang

scrnaseqpipeline

scrnaseq_benchmark

Bench-marking classification tools for scRNA-seq data

scrnaseq_cell_cluster_labeling

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

scrnaseq_pipelines

Drop-seq1: pipelines to process scRNA-seq data