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http://hipathdb.kobic.re.kr/

hiPathDB is an integrated pathway database that combines the curated human pathway data of NCI-Nature PID, Reactome, BioCarta and KEGG. In total, it includes 1661 pathways consisting of 8976 distinct physical entities. (2010.03.09) hiPathDB provides two different types of integration. The pathway-level integration, conceptually a simple collection of individual pathways, was achieved by devising an elaborate model that takes distinct features of four databases into account and subsequently reformatting all pathways in accordance with our model. The entity-level integration creates a single unified pathway that encompasses all pathways by merging common components. Even though the detailed molecular-level information such as complex formation or post-translational modifications tends to be lost, such integration makes it possible to investigate signaling network over the entire pathways and allows identification of pathway cross-talks. Another strong merit of hiPathDB is the built-in pathway visualization module that supports explorative studies of complex networks in an interactive fashion. The layout algorithm is optimized for virtually automatic visualization of the pathways.

Proper citation: hiPathDB - human integrated Pathway DB with facile visualization (RRID:SCR_008900) Copy   

•   Source: SciCrunch Registry

http://www.medinfopoli.polimi.it/GFINDer/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 16, 2019. Multi-database system providing large-scale lists of user-classified sequence identifiers with genome-scale biological information and functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves updated annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list, and calculates statistical significance values for each category. Moreover, GFINDer enables to functionally classify genes according to mined functional categories and to statistically analyze the obtained classifications, aiding in better interpreting microarray experiment results.

Proper citation: GFINDer: Genome Function INtegrated Discoverer (RRID:SCR_008868) Copy   

•   Source: SciCrunch Registry

http://hippocampome.org

A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.

Proper citation: Hippocampome.org (RRID:SCR_009023) Copy   

•   Source: SciCrunch Registry

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index

Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.

Proper citation: DIANA-LncBase (RRID:SCR_010840) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/placnet/

Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.

Proper citation: Placnet (RRID:SCR_024176) Copy   

•   Source: SciCrunch Registry

https://prinseq.sourceforge.net/

Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.

Proper citation: PRINSEQ (RRID:SCR_024178) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/poamsa/

Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.

Proper citation: POA (RRID:SCR_024172) Copy   

•   Source: SciCrunch Registry

https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index

Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.

Proper citation: PLIP (RRID:SCR_024173) Copy   

•   Source: SciCrunch Registry

https://github.com/COMBINE-lab/RapMap

Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping

Proper citation: rapmap (RRID:SCR_024204) Copy   

•   Source: SciCrunch Registry

http://rasmol.org/

Software package for molecular graphics visualisation.Used for visualisation of molecules.

Proper citation: rasmol (RRID:SCR_024208) Copy   

•   Source: SciCrunch Registry

https://github.com/silx-kit/pyFAI

Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.

Proper citation: pyFAI (RRID:SCR_024186) Copy   

•   Source: SciCrunch Registry

http://www.bmsc.washington.edu/raster3d/raster3d.html

Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.

Proper citation: Raster3D (RRID:SCR_024220) Copy   

•   Source: SciCrunch Registry

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

Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor.

Proper citation: Biobase (RRID:SCR_024224) Copy   

•   Source: SciCrunch Registry

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

Software R package to scrape data from Fitbit to generate graphs.

Proper citation: fitbitscraper (RRID:SCR_024273) Copy   

•   Source: SciCrunch Registry

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

Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data.

Proper citation: fitdistrplus (RRID:SCR_024274) Copy   

•   Source: SciCrunch Registry

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

Software R package for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling.

Proper citation: forecast (RRID:SCR_024277) Copy   

•   Source: SciCrunch Registry

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

Software R package as implementation of LexRank algorithm. Used for computing sentence importance based on concept of eigenvector centrality in graph representation of sentences.

Proper citation: lexrankr (RRID:SCR_024278) Copy   

•   Source: SciCrunch Registry

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

Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package.

Proper citation: DT (RRID:SCR_024270) Copy   

•   Source: SciCrunch Registry

https://github.com/rvalieris/parallel-fastq-dump

Software wrapper to speed up downloading process by dividing the work into multiple threads.

Proper citation: parallel-fastq-dump (RRID:SCR_024150) Copy   

•   Source: SciCrunch Registry

https://github.com/FlorianThibord/OptimiR

Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.

Proper citation: OptimiR (RRID:SCR_024149) Copy   

•   Source: SciCrunch Registry