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http://jefferis.github.io/nat/
Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_016716) Copy
Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems.
Proper citation: BD FACS Sortware sorter software (RRID:SCR_016722) Copy
Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap.
Proper citation: VectorMap (RRID:SCR_016721) Copy
http://www.nbtltd.com/products/smi-begaze%E2%84%A2-analysis-software
Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results.
Proper citation: SMI BeGaze (RRID:SCR_016648) Copy
Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data.
Proper citation: circular statistics (RRID:SCR_016651) Copy
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
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
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
Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.
Proper citation: PaVE (RRID:SCR_016599) Copy
https://tbportals.niaid.nih.gov
Web based open access platform for global drug resistant tuberculosis data sharing and analysis. The NIAID TB Portals program and consortium of clinicians and scientists from countries with a heavy burden of TB, especially drug resistant TB, to collect TB data.
Proper citation: TB PORTALS (RRID:SCR_016594) Copy
https://www.ncbi.nlm.nih.gov/orffinder
Software tool to search for open reading frames (ORFs) in the DNA sequence. The program returns the range of each ORF, along with its protein translation. Used to search newly sequenced DNA for potential protein encoding segments, verify predicted protein. Limited to the subrange of the query sequence up to 50 kb long.
Proper citation: Open Reading Frame Finder (RRID:SCR_016643) Copy
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
https://www.bioconductor.org/packages/release/workflows/html/RnaSeqGeneEdgeRQL.html
Software to study analysis of an RNA-Seq experiment using the Rsubread and edgeR packages. The workflow starts from read alignment and continues on to data exploration, to differential expression and, finally, to pathway analysis. The analysis includes plots, GO and KEGG analyses, and the analysis of a expression signature as generated by a prior experiment.
Proper citation: RnaSeqGeneEdgeRQL (RRID:SCR_016699) Copy
https://bioinformatics.niaid.nih.gov/hasp
Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins.
Proper citation: HASP (RRID:SCR_016615) Copy
https://sleepdata.org/datasets/ccshs
Portal for population based pediatric cohorts studied with objective sleep studies. Includes children with in-home sleep studies, acoustic reflectometry, anthropometry, spirometry, blood pressure (BP), and neuropsychology (NP) and behavioral assessments. Signals recorded include EEG, ECG, EOG, EMG, SpO2, airflow (thermocouple) nasal pressure, respiratory effort, position, plethysmography, light, HR.
Proper citation: Cleveland Children's Sleep and Health Study (RRID:SCR_016584) Copy
https://sleepdata.org/datasets/bestair/
Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume.
Proper citation: Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) Copy
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
https://github.com/kendomaniac/rCASC
Software package for reproducible classification analysis of single cell sequencing data.
Proper citation: rCASC (RRID:SCR_017005) Copy
Software tool for data management in clinical studies to improve care for patients with Traumatic Brain Injury (TBI). Used to search and find study variables with the associated information and export study data for further analysis.
Proper citation: INCF-Neurobot (RRID:SCR_017004) Copy
https://www.stemformatics.org/#
Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.
Proper citation: Stemformatics (RRID:SCR_017002) Copy
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