Tools   Select Another Resource Report Type

https://github.com/aroth85/pyclone

Software tool to infer the prevalence of point mutations in heterogeneous cancer samples. Probabilistic model for inferring clonal population structure from deep NGS sequencing.

Proper citation: Pyclone (RRID:SCR_016873) Copy   

•   Source: SciCrunch Registry

https://github.com/reinkk/Metab

Software package as a metabolomic data processing pipeline in R codes.

Proper citation: Metab (RRID:SCR_016877) Copy   

•   Source: SciCrunch Registry

https://github.com/PatternRecognition/OpenBMI

Software package for the development of Brain-Computer Interfaces with advanced pattern recognition algorithms. Used for analyzing brain signals which can be used to acquire, filter, process, classify and visualize brain signals in real time.

Proper citation: OpenBMI (RRID:SCR_016876) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/phenograph

Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity.

Proper citation: Phenograph (RRID:SCR_016919) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Proper citation: clusterProfiler (RRID:SCR_016884) Copy   

•   Source: SciCrunch Registry

http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home

Software package for processing and analysis of EM images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools.

Proper citation: Appion Package (RRID:SCR_016734) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html

Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.

Proper citation: RnaSeqGeneEdgeRQL (RRID:SCR_016699) Copy   

•   Source: SciCrunch Registry

http://ced.co.uk/products/sigovin

Software package for sweep based data acquisition and analysis of time based waveform data obtained through CED digital analogue converter by Cambridge Electronic Design System Limited. Used for transient capture, patch and voltage clamp, LTP studies, evoked response and TMS.

Proper citation: Signal (RRID:SCR_017081) Copy   

•   Source: SciCrunch Registry

https://github.com/LabTranslationalArchitectomics/RiboWaltz

Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.

Proper citation: riboWaltz (RRID:SCR_016948) Copy   

•   Source: SciCrunch Registry

https://github.com/kendomaniac/rCASC

Software package for reproducible classification analysis of single cell sequencing data.

Proper citation: rCASC (RRID:SCR_017005) Copy   

•   Source: SciCrunch Registry

http://scikit-criteria.org/en/latest/

Software tool as collection of Multiple Criteria Decision Analysis methods integrated into scientific Python stack.

Proper citation: Scikit-Criteria (RRID:SCR_017084) Copy   

•   Source: SciCrunch Registry

https://github.com/lucapinello/Haystack

Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline.

Proper citation: Haystack (RRID:SCR_017087) Copy   

•   Source: SciCrunch Registry

http://zhoulab.usc.edu/TopDom/

Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TopDom (RRID:SCR_016964) Copy   

•   Source: SciCrunch Registry

http://www.lipidontology.com

Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way.

Proper citation: LION/web (RRID:SCR_017018) Copy   

•   Source: SciCrunch Registry

https://anima.irisa.fr

Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows.

Proper citation: Anima (RRID:SCR_017017) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/gage/

Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.

Proper citation: GAGE (RRID:SCR_017067) Copy   

•   Source: SciCrunch Registry

http://crispr.hzau.edu.cn/CRISPR/

Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.

Proper citation: CRISPR-P (RRID:SCR_016941) Copy   

•   Source: SciCrunch Registry

https://team.inria.fr/empenn/

Project between Inria, Inserm, CNRS, and University of Rennes for biomedical image analysis for understanding neurological disease. Used to diagnose, monitor and deliver treatment for mental, neurological and substance use disorders by establishing multidisciplinary team between information sciences and medicine in medical imaging, neuroinformatics and population cohorts.

Proper citation: Empenn (RRID:SCR_017074) Copy   

•   Source: SciCrunch Registry

https://github.com/llawas/Rice_HxD_Metabolomics

Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress.

Proper citation: Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) Copy   

•   Source: SciCrunch Registry

https://github.com/Inria-Visages/Anima-Scripts-Public

Open source scripts for medical image processing. Provides set of scripts in Python shell. These scripts use essentially tools from Anima to perform more complex series like image preprocessing, model estimation, atlas creation.

Proper citation: Anima scripts (RRID:SCR_017072) Copy   

•   Source: SciCrunch Registry