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https://brainlife.io/docs/using_ezBIDS/

Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms.

Proper citation: ezBIDS (RRID:SCR_025563) Copy   

•   Source: SciCrunch Registry

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.uwyo.edu/buerkle/software/bamova/

Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

Proper citation: bamova (RRID:SCR_000510) Copy   

•   Source: SciCrunch Registry

http://www.stanford.edu/group/Urchin/contents.html

Laboratory modules designed for high school students covering sea urchin embryology including fertilization and development.

Proper citation: Sea Urchin Embryology (RRID:SCR_000460) Copy   

•   Source: SciCrunch Registry

http://www.cs.utah.edu/~miriah/pathline/Overview.html

Software visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species.

Proper citation: Pathline (RRID:SCR_000635) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/LOVE

A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html

Proper citation: LONI Visualization Tool (RRID:SCR_000765) Copy   

•   Source: SciCrunch Registry

http://megasoftware.net/

Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Proper citation: MEGA (RRID:SCR_000667) Copy   

•   Source: SciCrunch Registry

http://zoobank.org/

A database of scientific names in zoology. ZooBank is an online, open-access, community-generated registry for zoological nomenclature. It serves as a service to taxonomists, biologists, and the global diversity informatics community. It is the Official Register of the International Commission on Zoological Nomenclature (ICZN).

Proper citation: ZooBank (RRID:SCR_000901) Copy   

•   Source: SciCrunch Registry

http://lamp.icsi.berkeley.edu/lamp/

A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown.

Proper citation: Local Ancestry in adMixed Populations (RRID:SCR_001258) Copy   

•   Source: SciCrunch Registry

http://bmcmicrobiol.biomedcentral.com/articles/10.1186/1471-2180-9-S1-S1

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2016. A consortium that created universal descriptors to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. The organization uses a controlled vocabulary to set a process in place to describe plant associated microbes and their interactions with their plant-hosts. These higher order terms can describe gene products of all types of symbionts (e.g. parasites, commensals, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. This initiative is a multi-institutional collaborative effort to pool information and research in: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla.

Proper citation: PAMGO (RRID:SCR_000022) Copy   

•   Source: SciCrunch Registry