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https://github.com/voutcn/megahit
Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server.
Proper citation: MEGAHIT (RRID:SCR_018551) Copy
https://github.com/BGI-Qingdao/TGS-GapCloser
Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes.
Proper citation: TGS-GapCloser (RRID:SCR_017633) Copy
https://github.com/brentp/mosdepth
Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.
Proper citation: mosdepth (RRID:SCR_018929) Copy
https://github.com/AnacletoLAB/parSMURF
Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants.
Proper citation: parSMURF (RRID:SCR_017560) Copy
https://github.com/hms-dbmi/EHRtemporalVariability
Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.
Proper citation: EHRtemporalVariability (RRID:SCR_018663) Copy
Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.
Proper citation: PyBEL (RRID:SCR_017660) Copy
https://github.com/nch-igm/rna-stability
Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species.
Proper citation: rna-stability (RRID:SCR_019259) Copy
https://radar-base.org/index.php/home/about-us/
Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way.
Proper citation: RADAR-base (RRID:SCR_019233) Copy
http://topaz.gatech.edu/GeneMark/
Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.
Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy
https://amp.pharm.mssm.edu/geneshot/
Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.
Proper citation: Geneshot (RRID:SCR_017582) Copy
Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available.
Proper citation: Mousebytes (RRID:SCR_017904) Copy
Software tool to obtain structural guidance in biocatalytic investigations. Program for molecular visualising, modelling, and dynamics. Initial stage YASARA View is for free while higher stages YASARA Model, YASARA Dynamics, YASARA Structure require license fee. Program for Windows, Linux, MacOS and Android. YASARA View is available for free and contains all functions to explore macromolecular structure interactively.
Proper citation: YASARA (RRID:SCR_017591) Copy
Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers.
Proper citation: AmoebaDB (RRID:SCR_017592) Copy
https://github.com/TomSexton00/4See
Software tool to visualize 4C data.
Proper citation: 4See (RRID:SCR_018014) Copy
https://github.com/srp33/ShinyLearner
Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data.
Proper citation: ShinyLearner (RRID:SCR_017608) Copy
https://github.com/shanemomara/omaraneurolab/tree/master/NeuroChaT
Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories.
Proper citation: NeuroChaT (RRID:SCR_018020) Copy
https://github.com/PapenfussLab/bionix
Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language.
Proper citation: BioNix (RRID:SCR_017662) Copy
https://github.com/hariszaf/pema
Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution.
Proper citation: PEMA (RRID:SCR_017676) Copy
Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser.
Proper citation: iTOL (RRID:SCR_018174) Copy
http://mummer.sourceforge.net/
Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.
Proper citation: MUMmer (RRID:SCR_018171) Copy
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