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https://github.com/zhouhj1994/LinDA

Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models.

Proper citation: LinDA (RRID:SCR_025966) Copy   

•   Source: SciCrunch Registry

https://github.com/kharchenkolab/conos

Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections.

Proper citation: Conos (RRID:SCR_026381) Copy   

•   Source: SciCrunch Registry

https://github.com/compgenomics/MeTPeak

Software package for finding the location of m6A sites in MeRIP-seq data.

Proper citation: MeTPeak (RRID:SCR_026533) Copy   

•   Source: SciCrunch Registry

https://github.com/YuningHao/FARDEEP

Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions.

Proper citation: FARDEEP (RRID:SCR_026704) Copy   

•   Source: SciCrunch Registry

https://github.com/DerrickWood/kraken2

Software tool as second version of Kraken taxonomic sequence classification system.

Proper citation: kraken2 (RRID:SCR_026838) Copy   

•   Source: SciCrunch Registry

https://github.com/KrishnaswamyLab/PHATE

Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances.

Proper citation: PHATE (RRID:SCR_027119) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.sdstate.edu/idep/

Integrated web application for differential expression and pathway analysis of RNA-Seq data.

Proper citation: iDEP: Integrated Differential Expression and Pathway analysis (RRID:SCR_027373) Copy   

•   Source: SciCrunch Registry

https://venomsbase-dashboard.shinyapps.io/VenomLanding/

Open-access, browser-based visualization and summary tool for venom transcriptomic and proteomic data. R Shiny–based interactive application designed as visualization and reporting interface for venom transcriptomic and proteomic data. It enables users to explore annotation metrics, toxin gene families, and quality-control summaries generated by analysis pipelines. While it will eventually serve as part of the VenomsBase front end, VenomView currently operates as standalone prototype. Provides interactive dashboards showing assembly quality, annotation scores, toxin gene families, and functional domains generated by the VenomFlow analysis pipeline. Connected to VenomLanding, VenomView currently features Doryteuthis pealeii (Squid), linking metadata with detailed annotation summaries. The expanded version will include Sepia bandensis (Cuttlefish), Octopus bimaculoides, and arachnid species.

Proper citation: VenomView (RRID:SCR_027588) Copy   

•   Source: SciCrunch Registry

https://github.com/McGranahanLab/TcellExTRECT

Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes.

Proper citation: T Cell ExTRECT (RRID:SCR_027742) Copy   

•   Source: SciCrunch Registry

https://github.com/vanallenlab/comut

Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.

Proper citation: CoMUT (RRID:SCR_027745) Copy   

•   Source: SciCrunch Registry

https://github.com/pyranges/ncls

Software library for nested containment list data structure for interval overlap queries, like interval tree. It is a static interval-tree that is fast for both construction and lookups.

Proper citation: Nested containment list (RRID:SCR_027849) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

http://sobekrepository.org/

Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.

Proper citation: SobekCM (RRID:SCR_003225) Copy   

•   Source: SciCrunch Registry

http://www.qgene.org/

A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

Proper citation: QGene (RRID:SCR_003209) Copy   

•   Source: SciCrunch Registry

http://compgen.bscb.cornell.edu/phast/

A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Proper citation: PHAST (RRID:SCR_003204) Copy   

•   Source: SciCrunch Registry

http://datasharing.net

The U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data.

Proper citation: Datasharing.net (RRID:SCR_003312) Copy   

•   Source: SciCrunch Registry

http://www.marine-geo.org/

Repository providing free access to marine geophysical data (e.g. bathymetry, seismic data, magnetics, gravity, images) and related land-based data from NSF-funded research conducted throughout the global oceans. Data Portals include GeoPRISMS, MARGINS, Ridge 2000, Antarctic and Southern Ocean Data Synthesis, the Global Multi-Resolution Topography Synthesis, and Seismic Reflection Field Data Portal. Primary data types served are multibeam bathymetric data from the ocean floor, seismic reflection data imaging below the seafloor, and multi-disciplinary ship based data from the Southern Ocean. Other holdings include deep-sea photographic transects, and ultra-high resolution bathymetry, temperature probe data, biological species compilations, MAPR and CTD data. Derived data products and sets include microseismicity catalogs, images, visualization scenes, magnetic and gravity compilations, grids of seismic layer thickness, velocity models, GIS project files, and 3D visualizations. Tools to discover, explore, and visualize data are available. They deliver catalogs, maps, and data through standard programmatic interfaces. GeoMapApp, a standalone data visualization and analysis tool, permits dynamic data exploration from a map interface and the capability to generate and download custom grids and maps and other data. Through GeoMapApp, users can access data hosted at the MGDS, at other data repositories, and import their own data sets. Global Multi-Resolution Topography (GMRT) is a continuously-updated compilation of seafloor bathymetry integrated with global land topography. It can be used to create maps and grids and it can be accessed through several standard programmatic interfaces including GeoMapApp and Google Earth. The GMRT compilation can also be explored in 3D using Virtual Ocean. The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based search options are provided. Each item in the MediaBank is accompanied by metadata that provides access to a cruise catalog and data repository.

Proper citation: Marine Geoscience Data System (RRID:SCR_002164) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

•   Source: SciCrunch Registry

http://nsidc.org/

National data center / repository for snow and ice data including snow, ice, glaciers, frozen ground, and climate interactions that make up Earth's cryosphere. The center manages and distributes scientific data, creates tools for data access, supports data users, performs scientific research, and educates the public about the cryosphere. Users may explore the Earth's frozen places in the collection of photographs and images. Photographs from field research trips, images captured by satellites of the changing cryosphere, and photos and images are available. Data sets are organized into the following groups: sea ice, frozen ground, snow cover, snow hydrology, glaciers and ice sheets, arctic people.

Proper citation: National Snow and Ice Data Center (RRID:SCR_002220) Copy   

•   Source: SciCrunch Registry

http://www.opentopography.org/

Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development

Proper citation: OpenTopography (RRID:SCR_002204) Copy   

•   Source: SciCrunch Registry