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https://github.com/WilsonSayresLab/XYalign

Software tool for identifying, understanding, and correcting technical biases on the sex chromosomes in next generation sequencing data.

Proper citation: XYalign (RRID:SCR_016661) Copy   

•   Source: SciCrunch Registry

https://utex.org/

The UTEX Culture Collection of Algae includes different strains of living algae, representing most major taxa. Cultures in the Collection are used for research, teaching, biotechnology development, and various other projects throughout the world.

Proper citation: Culture Collection of Algae at the University of Texas (RRID:SCR_016782) Copy   

•   Source: SciCrunch Registry

https://loompy.org

Python implementation of the Loom file format to store and organize very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations and sparse graph objects. Used to store single-cell gene expression data. Official Python library (API) used to create, read, and manipulate .loom files, supporting out-of-memory operations to handle datasets larger than RAM.

Proper citation: LoomPy (RRID:SCR_016666) Copy   

•   Source: SciCrunch Registry

http://www.ccb.jhu.edu/software/centrifuge/

Software for rapid and sensitive classification of metagenomic sequences. Used for the classification of DNA sequences from microbial samples and analysis of large metagenomics data sets on conventional desktop computers.

Proper citation: Centrifuge Classifier (RRID:SCR_016665) Copy   

•   Source: SciCrunch Registry

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://blake.bcm.edu/emanwiki/EMAN2

Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography.

Proper citation: EMAN (RRID:SCR_016867) 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://knoweng.org

Part of the NIH Big Data to Knowledge (BD2K) Initiative. One of 11 Centers of Excellence in Big Data Computing. Platform for genomics data analysis where user-supplied data sets will be analyzed in the context of existing knowledge. E-science framework for genomics where biomedical scientists will have access to powerful methods of data mining, network mining, and machine learning to extract knowledge out of genomics data.

Proper citation: KnowEnG (RRID:SCR_016875) 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

https://csgid.org/csgid/metal_sites

Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal.

Proper citation: CheckMyMetal (RRID:SCR_016887) Copy   

•   Source: SciCrunch Registry

http://www.wrbu.org/index.html

National resource for systematics research on medically important arthropods and maintainance of the U.S. mosquito collection based in the Smithsonian Institution. Provides an online repository for vector collection data and clearinghouse where individuals and organizations can contribute vector occurrence records, search for vector information, and use tools for the visualization of various vector collections.

Proper citation: Walter Reed Biosystematics Unit (RRID:SCR_016729) 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://www.nitrc.org/projects/quicknii/

Histological brain section series aligner to volumetric atlases. Software tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems. Part of the QUINT workflow.

Proper citation: QuickNII (RRID:SCR_016854) Copy   

•   Source: SciCrunch Registry

http://grigoriefflab.janelia.org/ctffind4

Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4.

Proper citation: CTFFIND (RRID:SCR_016732) Copy   

•   Source: SciCrunch Registry

https://github.com/TGAC/KAT

Software that generates, analyses and compares k-mer spectra produced from sequence files. Used to quality control NGS datasets and genome assemblies.

Proper citation: KAT (RRID:SCR_016741) 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

http://southgreen.fr/content/gigwa

Web tool to explore genotyping metdata by filtering it on basis of variant features, including functional annotations and matching genotype patterns. May be deployed on workstation or as data portal. Allows to feed MongoDB database with VCF, PLINK or HapMap files and provides interface to filter data in real time. Used to export filtered data into formats and features connectivity with online genomic tools and with standalone software such as FlapJack or IGV. Gigwa hosted datasets are interoperable via two standard REST APIs such GA4GH and BrAPI.

Proper citation: Gigwa (RRID:SCR_017080) 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