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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
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
http://www.cbs.dtu.dk/services/RNAmmer/
Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.
Proper citation: RNAmmer (RRID:SCR_017075) Copy
https://github.com/nolanlab/VORTEX
Software Java graphical tool for single cell analysis, clustering and visualization. Provides multithreaded implementations of clustering algorithms, including nonparametric density based X shift, Hierarchical clustering, Mean shift and K medoids.
Proper citation: VORTEX (RRID:SCR_017047) Copy
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
https://github.com/NIMML/ENISI-MSM
Software tool for simulating the mucosal immune responses to Helicobacter pylori infection in stomach.
Proper citation: ENteric Immunity SImulator (ENISI) Multi scale model (RRID:SCR_016918) Copy
https://github.com/dodomorandi/hatspil
Software Python tool for high throughput sequencing analysis, focused on high reliability, modularity and customisability.
Proper citation: HaTSPiL (RRID:SCR_017059) Copy
https://bioportainer.github.io/BioPortainer/
Open source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application.
Proper citation: BioPortainer (RRID:SCR_017058) Copy
Software R package for calculating, applying, evaluating and plotting results of polygenic risk scores analysis. Performs simulation study to estimate P value significance threshold for high resolution PRS studies and produces plots for inspection of results. Operating Unix/Linux.
Proper citation: PRSice (RRID:SCR_017057) Copy
Project to ethically obtain and evaluate human kidney biopsies from participants with Acute Kidney Injury (AKI) or Chronic Kidney Disease (CKD), create a kidney tissue atlas, define disease subgroups, and identify critical cells, pathways, and targets for novel therapies. Used to develop the next generation of software tools to visualize and understand the various components of kidney diseases and to optimize data collection. Multi site collaboration comprised of patients, clinicians, and investigators from across the United States.
Proper citation: Kidney Precision Medicine Project (RRID:SCR_016920) Copy
https://github.com/Frederik-D-Weber/cosleep
Software Python tool for sleep EEG analysis. Used for Closed and Open loop in Slow Ocillations, Sleep Stimulation in Auditory or Recording in full PSG using OpenBCI Cyton.
Proper citation: COsleep (RRID:SCR_017053) Copy
https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
Software tool for trimming and filtering sequencing data. Used to combine data quality related trimming, filtering, and masking operations into a single tool adapter. BBDuk2 allows multiple kmer based operations in a single pass.
Proper citation: Bestus Bioinformaticus Duk (RRID:SCR_016969) Copy
Software tool to create and provide heat maps through a graphical interface. Allows to create an expression, pairwise comparison, image overlay, geomap, and geocoordinate heat maps for different data types and applications. Used to interactively visualize data.
Proper citation: Heatmapper (RRID:SCR_016974) Copy
Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz.
Proper citation: Prism Clinical Imaging (RRID:SCR_016977) Copy
Project provides tools and knowledge to maximize the impact of the biological NMR studies. CCPN software facilitates data analysis and software integration. Project promotes the exchange of knowledge and provides training and best practices for the NMR community and has leading role in the development of NMR data sharing standard and coordination of NMR instrumentation proposals. Includes CCPN Data Model for macromolecular NMR and related areas, CcpNmr suite of programs like Analysis for spectrum visualization, resonance assignment and analysis, ChemBuild to create chemical structure templates in an NMR aware manner, FormatConverter for data exchange with common textual NMR formats and SpecView for swift, format independent peak and spectrum visualization.
Proper citation: Collaborative Computing Project for NMR (RRID:SCR_016983) Copy
https://github.com/macmanes-lab/BinPacker/blob/master/README
Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: BinPacker (RRID:SCR_017038) Copy
Genotype and phenotype database for maize images based on BioDIG. Supports multiple reference genomes and has been integrated with the MaizeGDB Genome Browser to make custom tracks showing mutant phenotypes within their genomic context. Allows for custom tagging of images to highlight regions related to the phenotypes. This is accomplished through an interface allowing users to create links from images to genomic coordinates and to curate and search images by gene model ID, gene symbol, and gene name.
Proper citation: Maize Database of Images and Genomes (RRID:SCR_016987) Copy
https://www.ccpn.ac.uk/v2-software/software/analysis
Software package for interactive NMR spectrum visualization, resonance assignment and data analysis. Graphical elements allow to enter information and to view status of data and library functions manipulate the CCPN data model objects to record the scientific information. Software is cross platform and works on Linux, Mac OSX, Windows and Unix.
Proper citation: CCPN Analysis (RRID:SCR_016984) Copy
https://github.com/INTABiotechMJ/MITE-Tracker
Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.
Proper citation: MITE-Tracker (RRID:SCR_017030) Copy
https://github.com/g2-bernotas/PS-Plant-Framework
Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters.
Proper citation: PS-Plant Framework (RRID:SCR_017032) Copy
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