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https://knowledge.figshare.com/plus

Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability.

Proper citation: FigsharePlus (RRID:SCR_021762) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://jspecies.ribohost.com/jspeciesws/#analyse

Web server for prokaryotic species circumscription based on pairwise genome comparison. Service for in silico calculating extent of identity between two genomes, parameter routinely used in process of polyphasic microbial species circumscription. Service measures average nucleotide identity.

Proper citation: JSpeciesWS (RRID:SCR_022059) Copy   

•   Source: SciCrunch Registry

https://www.trikinetics.com/Downloads/DAMSystem3%20Software%20Data%20Sheet.pdf

Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System.

Proper citation: TriKinetics DAMSystem3 Software (RRID:SCR_021809) Copy   

•   Source: SciCrunch Registry

http://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039

Browser for mouse developmental anatomy. Ontology of mouse developmental anatomy was originally developed by Jonathan Bard and his colleagues as part of Edinburgh Mouse Atlas Project (EMAP) in order to provide structured controlled vocabulary of stage specific anatomical structures for developing laboratory mouse.

Proper citation: Mouse Developmental Anatomy Ontology Browser (RRID:SCR_021808) Copy   

•   Source: SciCrunch Registry

https://github.com/jeffdaily/parasail

Software tool as multiple sequence alignement for global, local and semi global alignments.

Proper citation: PARASAIL (RRID:SCR_021805) Copy   

•   Source: SciCrunch Registry

http://www.lbgi.fr/~julie/LEON-BIS

Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc.

Proper citation: LEON BIS (RRID:SCR_021803) Copy   

•   Source: SciCrunch Registry

https://yanglab.nankai.edu.cn/trRosetta/

Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets.

Proper citation: trRosetta (RRID:SCR_021181) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/about

Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials.

Proper citation: RobotReviewer (RRID:SCR_021064) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/RNAProt

Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction.

Proper citation: RNAProt (RRID:SCR_021218) Copy   

•   Source: SciCrunch Registry

https://www.panda3d.org/

Open source game engine and framework for 3D rendering and game development for Python and C++ programs. Graphics engine and programming environment to support everything from real time graphics applications to development of high end virtual reality theme park attractions or video games.

Proper citation: Panda3D (RRID:SCR_021216) Copy   

•   Source: SciCrunch Registry

https://data.fmi.ch/

Data repository for Friedrich Miescher Institute for Biomedical Research in areas of epigenetics, quantitative biology, and neurobiology.

Proper citation: Friedrich Miescher Institute data repository (RRID:SCR_021214) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/iris-scanning/

Software LabView package for two-photon calcium imaging acquisition. Used for controlling two-photon microscope and preprocessing of calcium imaging data.

Proper citation: IRIS two photon acquisition package (RRID:SCR_021212) Copy   

•   Source: SciCrunch Registry

https://chanzuckerberg.com/science/programs-resources/single-cell-biology/cellxgene/

Software tool as interactive explorer for single cell transcriptomics datasets. Used to explore and visualize high dimensional single cell datasets in interactive way. Can visualize gene expression at level of entire dataset or particular subset of cells to help identify cell types, which can in turn help identify diseases. Enables plotting gene expression level against another gene to compare how these different genes are expressed across dataset. Open source cell visualization tool integrates with tools like SciPy and Jupyter.

Proper citation: cellxgene (RRID:SCR_021059) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/p/iris-scanning/calliope

Software package for image processing for MATLAB. Used for processing of calcium imaging data.

Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy   

•   Source: SciCrunch Registry

https://github.com/slimsuite/depthsizer

Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size.

Proper citation: DepthSizer (RRID:SCR_021232) Copy   

•   Source: SciCrunch Registry

https://github.com/Danis102/seqpac

Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis.

Proper citation: seqpac (RRID:SCR_021079) Copy   

•   Source: SciCrunch Registry

https://github.com/chhylp123/hifiasm

Software tool as haplotype resolved de novo assembler for PacBio Hifi reads. Can assemble human genome in several hours.Introduces new graph binning algorithm and achieves haplotype resolved assembly given trio data. Takes advantage of long high fidelity sequence reads to represent haplotype information in phased assembly graph. Preserves contiguity of all haplotypes.

Proper citation: Hifiasm (RRID:SCR_021069) Copy   

•   Source: SciCrunch Registry

Issue

https://biology-assets.anu.edu.au/GenAlEx/Welcome.html

Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level.

Proper citation: GenAlEx (RRID:SCR_021102) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/fgsea/

Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Proper citation: fgsea (RRID:SCR_020938) Copy   

•   Source: SciCrunch Registry