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https://github.com/r3fang/SnapTools

Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.

Proper citation: SnapTools (RRID:SCR_018097) Copy   

•   Source: SciCrunch Registry
  

https://www.gisaid.org/

Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data.

Proper citation: Global Initiative on Sharing All Influenza Data (RRID:SCR_018251) Copy   

•   Source: SciCrunch Registry
  

https://www.astropy.org

Community software Pyton library for astronomy. Collection of software packages written in Python programming language for use in astronomy. Package contains key functionality and common tools needed for performing astronomy and astrophysics with Python. Core of Astropy Project, which aims to enable community to develop ecosystem of Affiliated Packages covering broad range of needs for astronomical research, data processing, and data analysis.

Proper citation: astropy (RRID:SCR_018148) Copy   

•   Source: SciCrunch Registry
  

https://tripod.nih.gov/curvefit/

Large scale dose response curve fitting and curve classification software. Automated curve fitting and classificatoin software. Web deployed software. Algorithm recognizes bell shaped curves, implements standard hill equation, extensible for other models.

Proper citation: NCGC CurveFit (RRID:SCR_018079) Copy   

•   Source: SciCrunch Registry
  

https://github.com/galaxyproteomics/mvpapplication-git.git

Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.

Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy   

•   Source: SciCrunch Registry
  

https://CRAN.R-project.org/package=biomod2

Software R package for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization.

Proper citation: biomod2 (RRID:SCR_018246) Copy   

•   Source: SciCrunch Registry
  

http://statistika.mfub.bg.ac.rs/interactive-linegraph/

Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.

Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy   

•   Source: SciCrunch Registry
  

https://huygens.science.uva.nl/PlotsOfData/

Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions.

Proper citation: PlotsOfData (RRID:SCR_018333) Copy   

•   Source: SciCrunch Registry
  

https://webs.iiitd.edu.in/raghava/coronavir

Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses.

Proper citation: CoronaVIR (RRID:SCR_018338) Copy   

•   Source: SciCrunch Registry
  

https://professional.diabetes.org/content-page/covid-19

Web page created by American Diabetes Association. Contains resources and information about COVID-19 for diabetes professionals and patients. ADA also provides online forum, webinar series and podcast. Online forum to exchange questions, answers, and best practices with leading clinicians from diabetes community. All ADA members can contribute, and any interested health professional can read forum and responses.

Proper citation: American Diabetes Association COVID-19 Resources and Webinar Series (RRID:SCR_018346) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/ena/pathogens/covid-19

Data collection related to COVID-19 held at EMBL-EBI , including sequences of outbreak isolates and records related to coronavirus biology, protein expression, protein sequence, protein structure, proteome and translatome data and literature.

Proper citation: EMBL-EBI Pathogens - COVID-19 (RRID:SCR_018343) Copy   

•   Source: SciCrunch Registry
  

https://bigd.big.ac.cn/ncov/?lang=en

Bioinformation related to COVID-19. Site developed and maintained by China National Center for Bioinformation. Collection of sequences, genome variations, publication, clinical resource data.

Proper citation: 2019 Novel Coronavirus Resource (2019nCoVR) by China National Center for Bioinformation (RRID:SCR_018342) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mcapuccini/mare

Software tool to leverage power of Docker and Spark to run and scale your serial tools in MapReduce fashion.

Proper citation: MaRe (RRID:SCR_018069) Copy   

•   Source: SciCrunch Registry
  

https://wholetale.org/

Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.

Proper citation: Whole Tale (RRID:SCR_017537) Copy   

•   Source: SciCrunch Registry
  

http://nhprtr.org/

Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species.

Proper citation: Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Waller-Lab/DiffuserCam

Software tool as processing code. Alternating direction method of multipliers (ADMM) algorithm for recovering 3D volumes from 2D raw data captured with DiffuserCam.

Proper citation: DiffuserCam (RRID:SCR_017466) Copy   

•   Source: SciCrunch Registry
  

https://www.drugabuse.gov

Portal provides list of genetic resources such as Brain Atlases and genomes for various species provided by National Institute of Drug Abuse.

Proper citation: Compilation of Genetics Resource Databases (RRID:SCR_017501) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cran/CopyNumber450kCancer

Software R package baseline correction for accurate copy number calling from 450k methylation array. Baseline correction for copy number data from cancer samples. Implements maximum density peak estimation (MDPE) method together with interactive reviewing to efficiently correct baseline in cancer samples.

Proper citation: CopyNumber450kCancer (RRID:SCR_017965) Copy   

•   Source: SciCrunch Registry
  

http://www.proteometools.org/index.php?id=home

Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.

Proper citation: ProteomeTools (RRID:SCR_018535) Copy   

•   Source: SciCrunch Registry
  

https://github.com/bjohnnyd/fs-tool

Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes.

Proper citation: fs-tool (RRID:SCR_018250) Copy   

•   Source: SciCrunch Registry