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http://genomespace.org

Interoperability framework which supports integrative genomics analysis via access to various bioinformatics tools. Rather than performing analyses itself, GenomeSpace acts as a hub for data from supported bioinformatics tools and reformats data and results when necessary.

Proper citation: GenomeSpace (RRID:SCR_014967) Copy   

•   Source: SciCrunch Registry

https://github.com/smithlabcode/riborex

Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.

Proper citation: riborex (RRID:SCR_019104) Copy   

•   Source: SciCrunch Registry

https://www.cbcb.umd.edu/software/epiviz

Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data.

Proper citation: Epiviz (RRID:SCR_022796) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/Maaslin2.html

SoftwareR package that identifies microbial taxa correlated with factors of interest using generalized linear models and mixed models.Used for efficiently determining multivariable association between clinical metadata and microbial meta'omic features.

Proper citation: MaAsLin2 (RRID:SCR_023241) Copy   

•   Source: SciCrunch Registry

https://github.com/ParkerLab/ataqv

Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments.

Proper citation: ataqv (RRID:SCR_023112) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/SURVIVOR

Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering.

Proper citation: SURVIVOR (RRID:SCR_022995) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/merqury

Software toolkit for reference free quality, completeness, and phasing assessment for genome assemblies. Genome assembly quality evaluation based on k-mers.

Proper citation: Merqury (RRID:SCR_022964) Copy   

•   Source: SciCrunch Registry

https://github.com/virajbdeshpande/AmpliconArchitect

Software package designed to call circular DNA from short read WGS data.Used to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates architecture of amplicon.Used to reconstruct structure of focally amplified regions using whole genome sequencing and validate it extensively on multiple simulated and real datasets, across wide range of coverage and copy numbers.

Proper citation: AmpliconArchitect (RRID:SCR_023150) Copy   

•   Source: SciCrunch Registry

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

Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.

Proper citation: ComplexUpset (RRID:SCR_022752) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry

https://upset.app/#:~:text=UpSet%20plots%20the%20intersections%20of,is%20part%20of%20an%20intersection.

Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.

Proper citation: UpSet (RRID:SCR_022731) Copy   

•   Source: SciCrunch Registry

https://github.com/walaj/svaba

Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.

Proper citation: SvABA (RRID:SCR_022998) Copy   

•   Source: SciCrunch Registry

https://upsetplot.readthedocs.io/en/stable/

Software Python implementation of UpSet plots to visualize set overlaps.

Proper citation: UpSetPlot (RRID:SCR_023225) Copy   

•   Source: SciCrunch Registry

http://crispor.tefor.net

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

Proper citation: CRISPOR (RRID:SCR_015935) Copy   

•   Source: SciCrunch Registry

https://cells.ucsc.edu/

Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.

Proper citation: UCSC Cell Browser (RRID:SCR_023293) Copy   

•   Source: SciCrunch Registry

https://github.com/hetio/hetmatpy

Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.

Proper citation: HetMatPy (RRID:SCR_023409) Copy   

•   Source: SciCrunch Registry

https://github.com/tobiasrausch/alfred

Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.

Proper citation: Alfred (RRID:SCR_023354) Copy   

•   Source: SciCrunch Registry

https://pathvisio.org/

Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins.

Proper citation: PathVisio (RRID:SCR_023789) Copy   

•   Source: SciCrunch Registry

http://avis.princeton.edu/pixie/index.php

bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it).

Proper citation: bioPIXIE (RRID:SCR_004182) Copy   

•   Source: SciCrunch Registry

http://life.ccs.miami.edu/life/

LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal.

Proper citation: LINCS Information Framework (RRID:SCR_003937) Copy   

•   Source: SciCrunch Registry