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raspa2

Classical molecular simulation code

rdata-project-manipulation

FPKM data manipulation with NCBI GEO data sets

rdkit

The official sources for the RDKit library

refinery-platform

The Refinery Platform is a data management, analysis and visualization system

ringspy

A Python automated geometric generation tool that generates 3D meshes of prismatic cellular solids with radial growth rules based on Voronoi diagrams.

rna-seq-in-the-cloud

An Easy to Use Analysis System for All Human Public bulk RNAseq Data!

rnalysis

RNA sequencing analysis pipeline

rnaseq_workflow

snakemake workflow for bulk RNA-seq workflow using STAR-edgeR

robotics_python

Robotics Mathematical modeling and theory with Python (learning through extensive numerical simulations and animations.)

rssalib

A library for stochastic simulation of complex biochemical reactions

salmon

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

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

sbml-test-suite

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.

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

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