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http://bioconductor.org/packages/GenomicFeatures/

Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database.

Proper citation: GenomicFeatures (RRID:SCR_016960) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenSMFS/FRETBursts

Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data.

Proper citation: FRETBursts (RRID:SCR_016898) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/GenomicRanges/

Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome.

Proper citation: Genomic Ranges (RRID:SCR_017051) Copy   

•   Source: SciCrunch Registry

https://knights-lab.github.io/MLRepo/

Machine learning repository for microbiome datasets.

Proper citation: ML Repo (RRID:SCR_017079) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/EpiEstim/index.html

Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series.

Proper citation: EpiEstim (RRID:SCR_018538) Copy   

•   Source: SciCrunch Registry

https://github.com/SouthGreenPlatform/metaXplor

Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures.

Proper citation: metaXplor (RRID:SCR_019025) Copy   

•   Source: SciCrunch Registry

https://github.com/constantAmateur/SoupX

Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.

Proper citation: SoupX (RRID:SCR_019193) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

Proper citation: DESeq2 (RRID:SCR_015687) Copy   

•   Source: SciCrunch Registry

https://cm.jefferson.edu/Off-Spotter//

Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers.

Proper citation: Off-Spotter (RRID:SCR_015739) Copy   

•   Source: SciCrunch Registry

https://github.com/sorgerlab/ashlar

Software for image processing of cyclic immunofluorescence data. It performs alignment by simultaneous harmonization of layer/adjacency registration.

Proper citation: ASHLAR (RRID:SCR_016266) Copy   

•   Source: SciCrunch Registry

https://github.com/PF2-pasteur-fr/SARTools

Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.

Proper citation: SARTools (RRID:SCR_016533) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

http://swift.cmbi.ru.nl/gv/hssp/

HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. Homologues are very likely to have the same 3D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of sequence aligned sequence families, but it is also a database of implied secondary and tertiary structures. Likely secondary structure are carried over from the PDB protein to each homologous protein. Tertiary structure models can be built by fitting the sequence of the homologue as aligned into the 3D template of the protein of known structure. Special software is needed to construct 3D models by homology, such WHATIF by Gert Vriend or MaxSprout by Liisa Holm and Chris Sander. The command rsync can be used to obtain a local copy of the HSSP. We appreciate receiving an Email from people who do so, but there are no strings attached. Everybody can freely download the files, academia and industry alike. If your institute''s firewall doesn''t allow you to use the (preferred) rsync way of obtaining HSSP files, feel free to work with FTP. The files are in that case available from: ftp://ftp.cmbi.ru.nl//pub/molbio/data/hssp/

Proper citation: HSSP (RRID:SCR_004953) Copy   

•   Source: SciCrunch Registry

http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/

Sting Report is a database of amino acid sequences, structures, functions, and parameters. It allows users to easily extract from the Blue Star Sting Database detailed but focused information about an individual amino acid, which belongs to a structure described in a PDB file. The extracted information is presented as a series of GIF images and a table, which are generated by Blue Star Sting modules and contain values of up to 125 sequence/structure/function descriptors/parameters. The HTML page resulting from a query on Sting Report, containing the GIF images and the table, is printable, and can also be composed and visualized at a computer platform with elementary configuration.

Proper citation: STING Report (RRID:SCR_005121) Copy   

•   Source: SciCrunch Registry

http://www.ihop-net.org/UniPub/iHOP/

Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

Proper citation: Information Hyperlinked Over Proteins (RRID:SCR_004829) Copy   

•   Source: SciCrunch Registry

http://www.gomapman.org/

An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.

Proper citation: GoMapMan (RRID:SCR_005060) Copy   

•   Source: SciCrunch Registry

http://ahdb.ee.ncku.edu.tw/

Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms.

Proper citation: Apo and Holo structures DataBase (RRID:SCR_004800) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/bioproject

Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.

Proper citation: NCBI BioProject (RRID:SCR_004801) Copy   

•   Source: SciCrunch Registry