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https://github.com/Crick-CancerGenomics/ascat

Software R package to infer tumor purity, ploidy and allele-specific copy number profiles. It is platform and species independent, and works for both Illumina and Affymetrix SNP arrays, as well as for massively parallel sequencing data.

Proper citation: ascat (RRID:SCR_016868) Copy   

•   Source: SciCrunch Registry

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

http://bioconductor.org/packages/release/data/experiment/html/affydata.html

Software R package for analysis of Affymetrix Data. Contains samples data files of a large size.

Proper citation: affydata (RRID:SCR_016976) 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/kendomaniac/rCASC

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

Proper citation: rCASC (RRID:SCR_017005) Copy   

•   Source: SciCrunch Registry

https://immunedb.readthedocs.io/en/latest/

Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.

Proper citation: ImmuneDB (RRID:SCR_017125) Copy   

•   Source: SciCrunch Registry

https://github.com/Rinoahu/SwiftOrtho

Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.

Proper citation: SwiftOrtho (RRID:SCR_017122) 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

https://eda.nc3rs.org.uk/

Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility.

Proper citation: Experimental Design Assistant (RRID:SCR_017019) 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

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https://biit.cs.ut.ee/clustvis/

Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps.

Proper citation: ClustVis (RRID:SCR_017133) 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

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