Tools   Select Another Resource Report Type

https://github.com/msraredon/Connectome

Software R package for calculation and interactive exploration of cell-cell signaling network topologies contained in single-cell RNA-sequencing data. Used to explore cell-cell connectivity patterns based on ligand and receptor data in heterogeneous single-cell datasets.

Proper citation: Connectome (RRID:SCR_028632) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/SingleCellSignalR.html

Software tool to infer and map cell-to-cell communication networks using single-cell RNA sequencing (scRNA-seq) or proteomics data. Used for inference of intercellular networks from single-cell transcriptomics.

Proper citation: SingleCellSignalR (RRID:SCR_028633) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pip/

Software package installer for Python. You can use pip to install packages from the Python Package Index and other indexes.

Proper citation: pip (RRID:SCR_028591) Copy   

•   Source: SciCrunch Registry

https://github.com/palombom/SANDI-Matlab-Toolbox-Latest-Release

Software toolbox for estimation of MR signal fraction of brain cell bodies (of all cell types, from neurons to glia, namely soma) and cell projections (of all cell types, from dentrites and myelinated axons to glial processes, namely neurties ) as well as apparent MR cell body radius and intraneurite and extracellular apparent diffusivities from a suitable diffusion-weighted MRI acquisition using Machine Learning.

Proper citation: SANDI Matlab Toolbox (RRID:SCR_028525) Copy   

•   Source: SciCrunch Registry

https://github.com/openvax/mhcflurry

Software MHC I ligand prediction package with competitive accuracy and documented implementation. Used for peptide-MHC I binding affinity prediction.

Proper citation: mhcflurry (RRID:SCR_028577) Copy   

•   Source: SciCrunch Registry

https://github.com/VanLoo-lab/ASCAT.sc

Software application as implementation of ASCAT allowing generation of CNV profiles from single cell and short coverage sequencing data.

Proper citation: ASCAT sc (RRID:SCR_028613) Copy   

•   Source: SciCrunch Registry

https://github.com/markowetzlab/CINSignatureQuantification

Software R package to quantify the activity of signatures of chromosomal instability from absolute copy number profiles. Used to quantifying copy number signatures from absolute copy number profiles.

Proper citation: CINSignatureQuantification (RRID:SCR_028614) Copy   

•   Source: SciCrunch Registry

http://www.pmda.go.jp/english/

A Japanese regulatory government agency which regulates the safety, efficacy and quality of pharmaceuticals and medical devices in order to protect the public health of the people. The agency plays three main roles: drug and medical device testing, post-marketing drug safety, and victim compensation for those affected by adverse drug reactions from pharmaceuticals or other biological products. It is an incorporated administrative agency with non-civil service status.

Proper citation: Pharmaceuticals and Medical Devices Agency (RRID:SCR_000244) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/webtools/tapir/

Web server designed for prediction of plant microRNA targets.

Proper citation: TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) Copy   

•   Source: SciCrunch Registry

http://www.tripos.com/index.php?family=modules,SimplePage,surflex_dock

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software program that screens large libraries of compounds including ligands, and their docking.

Proper citation: Surflex-Dock (RRID:SCR_000196) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/src/contrib/Archive/MetaDE/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.

Proper citation: MetaDE (RRID:SCR_000199) Copy   

•   Source: SciCrunch Registry

http://iclab.life.nctu.edu.tw/iclab_webtools/sodock/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.

Proper citation: SODOCK (RRID:SCR_000193) Copy   

•   Source: SciCrunch Registry

http://exon.gatech.edu/paul/unsplicer/index.htm

An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight.

Proper citation: UnSplicer (RRID:SCR_000226) Copy   

•   Source: SciCrunch Registry

https://github.com/matteocereda/RNAmotifs

Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.

Proper citation: RNAmotifs (RRID:SCR_000263) Copy   

•   Source: SciCrunch Registry

http://www.utmb.edu/

A division of the University of Texas that is dedicated to medical education.

Proper citation: University of Texas Medical Branch at Galveston (RRID:SCR_000144) Copy   

•   Source: SciCrunch Registry

http://www.upm.es/internacional

A public technical university in Madrid with progams at the undergraduate, graduate and postdoctorate level in fields such as architecture and mining in addition to engineering in areas including forestry, agriculture, computer science and aeronautics.

Proper citation: Polytechnic University of Madrid; Madrid; Spain (RRID:SCR_000253) Copy   

•   Source: SciCrunch Registry

https://poznan.pan.pl/?page_id=1824&lang=en

An academy of sciences that is based in Poland. The academy is an important institution for the development of science research in Poland, in addition to being part of a larger network of research institutes.

Proper citation: Polish Academy of Sciences Poznan; Poznan; Poland (RRID:SCR_000248) Copy   

•   Source: SciCrunch Registry

http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.

Proper citation: miRanalyzer (RRID:SCR_000163) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/biogrinder/

An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Proper citation: Grinder (RRID:SCR_000168) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CNTools.html

Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

Proper citation: CNTools (RRID:SCR_000281) Copy   

•   Source: SciCrunch Registry