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https://github.com/ChristopherWilks/megadepth
Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts.
Proper citation: Megadepth (RRID:SCR_022779) Copy
Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers.
Proper citation: ZDOCK Server (RRID:SCR_022518) Copy
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
http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/
Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.
Proper citation: VirtualPlant (RRID:SCR_022576) Copy
http://www.evidenceontology.org
A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2
Proper citation: ECO (RRID:SCR_002477) Copy
https://github.com/vpc-ccg/svict
Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA.
Proper citation: SViCT (RRID:SCR_023656) Copy
Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR.
Proper citation: CRISPRscan (RRID:SCR_023777) Copy
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
https://github.com/vlink/marge
Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.
Proper citation: Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) Copy
http://sysbio.rnet.missouri.edu/3Drefine/
Interactive web server for efficient protein structure refinement with capability to perform web based statistical and visual analysis.
Proper citation: 3DRefine (RRID:SCR_021883) Copy
Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.
Proper citation: RegulonDB (RRID:SCR_003499) Copy
A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.
Proper citation: Seg3D (RRID:SCR_002552) Copy
https://health.uconn.edu/worm-lab/track-a-worm/
Open source system for quantitative assessment of C. Elegans locomotory and bending behavior. Used for quantitative behavioral analyses to understand circuit and gene bases of behavior. Constantly records and analyzes position and body shape of freely moving worm at high magnification.
Proper citation: Track-A-Worm (RRID:SCR_018299) Copy
https://www.biosimulations.org/
Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.
Proper citation: BioSimulations (RRID:SCR_018733) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
https://sourceforge.net/projects/timezone1/
Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.
Proper citation: TimeZone (RRID:SCR_018564) Copy
https://cole-trapnell-lab.github.io/monocle3/
Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points.
Proper citation: Monocle3 (RRID:SCR_018685) Copy
Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.
Proper citation: BpForms (RRID:SCR_018653) Copy
Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.
Proper citation: ObjTables (RRID:SCR_018652) Copy
Web service for querying or retrieving gene annotation data.
Proper citation: MyGene.info (RRID:SCR_018660) Copy
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