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https://github.com/bpucker/KIPEs

Software tool as automatic approach for identification of players in biosynthesis pathway. Used for automatic annotation of flavonoid biosynthesis steps in new transcriptome of genome sequence assembly. Various enzymes of entire metabolic networks can be identified if sufficient knowledge about functionally relevant amino acids is available.Combines comprehensive sequence similarity analyses with inspection of functionally relevant amino acid residues and domains in subjected peptide sequences.

Proper citation: Knowledge based Identification of Pathway Enzymes (RRID:SCR_022370) Copy   

•   Source: SciCrunch Registry

https://huttenhower.sph.harvard.edu/picrust/

Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.

Proper citation: PICRUSt2 (RRID:SCR_022647) Copy   

•   Source: SciCrunch Registry

https://napari.org/

Multi dimensional image viewer for Python. Used for browsing, annotating, and analyzing large multi dimensional images. Can be coupled to machine learning and image analysis tools enabling more user friendly automated analysis.

Proper citation: Napari (RRID:SCR_022765) Copy   

•   Source: SciCrunch Registry

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

Software package for removing biases across multiple Hi-C datasets. Properly handles Hi-C-specific decay of chromatin interaction frequencies with increasing distance between interacting regions.

Proper citation: multiHiCcompare (RRID:SCR_022368) Copy   

•   Source: SciCrunch Registry

https://gtca.github.io/muon/

Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python.

Proper citation: MUON (RRID:SCR_022804) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://pmbb.med.upenn.edu/

BioBank supports researchers by providing centralized access to large number of annotated blood and tissue samples.

Proper citation: University of Pennsylvania Perelman School of Medicine Penn Medicine BioBank Core Facility (RRID:SCR_022415) Copy   

•   Source: SciCrunch Registry

https://github.com/Whitlock-Group/HERBS

Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space.

Proper citation: Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) Copy   

•   Source: SciCrunch Registry

https://docs.airr-community.org/en/stable/datarep/rearrangements.html

Part of AIRR Data Model, defines annotations needed for rearrangements, which are sequences describing rearranged adaptive immune receptor chain (e.g., antibody heavy chain or TCR beta chain). Data for Rearrangement objects are stored as rows in tab delimited file and should be compatible with any TSV reader. Dataset is defined in this context as: TSV file, TSV with companion YAML file containing metadata, or directory containing multiple TSV files and YAML files.

Proper citation: Adaptive Immune Receptor Repertoire Rearrangement Schema (RRID:SCR_022592) Copy   

•   Source: SciCrunch Registry

https://orthovenn2.bioinfotoolkits.net/home

Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences.

Proper citation: OrthoVenn2 (RRID:SCR_022504) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/pavca/

Project related to tracking behavior. Used to identify subgroups of individuals that differentially attribute incentive value to food cue. Includes apparatus for studying Pavlovian conditioned approach behavior. Customized rat PavCA chambers are constructed based on modular devices purchased from Med-Associates. Code used to operate equipment and collect data was written using Med-Associates’ MEDSTATE programming language. This program is then loaded into Med-PC V operating program, also created by Med-Associates.

Proper citation: PavCA project (RRID:SCR_022508) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/timed-pressure-control/

System uses Arduino microcontroller to control relay module that operates solenoid valve which all sit in 3D printed housing. Solenoid works in conjunction with flowmeter regulator to allow for controlled flow of pressurized air into target. Timing of distensions is controlled via either custom Python based UI, or by triggered TTL pulse.Timed pressure control hardware and software used for delivery of air mediated distensions in animal models.

Proper citation: Timed pressure control hardware and software for delivery of air mediated distensions in animal models (RRID:SCR_022363) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/mmop/

Software tool as multi subject keypoint detection library for real time pose estimation.Used to track behavior of monkeys in natural environments, without disrupting their typical pattern of behavior. Deep learning software system for body, face, hands, and foot estimation in monkeys.

Proper citation: OpenPose (RRID:SCR_022362) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/trex/

Open source animal tracking software tool. Used to visually track movement of multiple animals at once.

Proper citation: TRex (RRID:SCR_022361) Copy   

•   Source: SciCrunch Registry

http://hollywood.mit.edu/exonscan/

Software framework for modeling sequence motifs based on maximum entropy principle.

Proper citation: ExonScan Web Server (RRID:SCR_022516) Copy   

•   Source: SciCrunch Registry

https://github.com/SGDDNB/ShinyCell

Software R package to create interactive Shiny based web applications to visualise single cell data via visualising cell information and/or gene expression on reduced dimensions e.g. UMAP, visualising coexpression of two genes on reduced dimensions, visualising distribution of continuous cell information e.g. nUMI / module scores using violin plots / box plots, visualising composition of different clusters / groups of cells using proportion plots and visualising expression of multiple genes using bubbleplots / heatmap.Shiny Interactive Web Apps for Single-Cell Data.

Proper citation: ShinyCell (RRID:SCR_022756) Copy   

•   Source: SciCrunch Registry

https://edspace.american.edu/openbehavior/project/dlstream/

Software tool enables closed loop behavioral experiments using deep learning based markerless, real time posture detection.Closed loop behavioral experiment toolkit using pose estimation of body parts.

Proper citation: DLStream (RRID:SCR_022359) Copy   

•   Source: SciCrunch Registry

https://github.com/LINCellularNeuroscience/VAME

Software Python tool to cluster behavioral signals obtained from pose estimation tools. Unsupervised probabilistic deep learning framework capable of finding behavioral motifs in pose estimation data. Capable of augmenting quantitative behavioral analyses of data derived from standard pose-estimation software packages. Written based on core functions from DeepLabCut, and readily works with pose data from that package. Can also work with data from other pose estimation packages such as SLEAP.

Proper citation: Variational Embedding of Animal Motion (RRID:SCR_022477) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ComplexUpset

Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries.

Proper citation: ComplexUpset (RRID:SCR_022752) Copy   

•   Source: SciCrunch Registry

https://zdock.umassmed.edu/

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   

•   Source: SciCrunch Registry