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http://cell-innovation.nig.ac.jp/maser/AllPipelines/P000001138_en.html

Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.

Proper citation: loadBAM2ge_db (RRID:SCR_015951) Copy   

•   Source: SciCrunch Registry

https://www.perkinelmer.com/product/harmony-5-1-office-hh17000012

Software tool designed by PerkinElmer for high content screening systems. Used to quantify complex cellular phenotypes. High content analysis software.

Proper citation: Harmony (RRID:SCR_023543) Copy   

•   Source: SciCrunch Registry

https://www.enroll-hd.org

Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments.

Proper citation: Enroll-HD (RRID:SCR_023300) Copy   

•   Source: SciCrunch Registry

https://github.com/pirovc/grimer

Software tool to perform analysis of microbiome studies and generates portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

Proper citation: GRIMER (RRID:SCR_023265) Copy   

•   Source: SciCrunch Registry

https://www.gehealthcare.com/products/advanced-visualization/all-applications/volume-viewer

Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets.

Proper citation: GE Volume Viewer (RRID:SCR_023417) Copy   

•   Source: SciCrunch Registry

https://github.com/vpc-ccg/svict

Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA.

Proper citation: SViCT (RRID:SCR_023656) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/SlideSeq_Pipeline/README/

Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay.

Proper citation: Slide-seq Pipeline (RRID:SCR_023379) Copy   

•   Source: SciCrunch Registry

http://www.proteomesoftware.com/products/scaffold/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments

Proper citation: Scaffold (RRID:SCR_014321) Copy   

•   Source: SciCrunch Registry

https://lookerstudio.google.com/

Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization.

Proper citation: Google Looker Studio (RRID:SCR_023549) Copy   

•   Source: SciCrunch Registry

http://www.vsh.com/products/mflt/index.asp

Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software.

Proper citation: ModFit LT (RRID:SCR_016106) Copy   

•   Source: SciCrunch Registry

https://github.com/IGGoncalves/PhysiCOOL

Software Python library tailored to perform model calibration studies with PhysiCell. Generalized framework for model Calibration and Optimization Of modeLing projects.

Proper citation: PhysiCOOL (RRID:SCR_023305) Copy   

•   Source: SciCrunch Registry

https://github.com/Nanostring-Biostats/GeomxTools/

Software package contains tools for analyzing data from NanoString GeoMx Digital Spatial Profiler. Provides functions to read, quality control and normalize starting from Nanostring DCC and PKC files generated from NanoString GeoMx DSP. Contains definition of NanoStringGeoMxSet class which inherits from Biobase’s ExpressionSet class and NanoStringRCCSet class.

Proper citation: NanoString GeoMx Tools (RRID:SCR_023424) Copy   

•   Source: SciCrunch Registry

https://github.com/AIRI-Institute/DeepCT

Software tool can learn complex interconnections of epigenetic features and infer unmeasured data from any available input. Can learn cell type-specific properties, build biologically meaningful vector representations of cell types, and utilize these representations to generate cell type-specific predictions of effects of non-coding variations in human genome.

Proper citation: DeepCT (RRID:SCR_023302) Copy   

•   Source: SciCrunch Registry

https://github.com/qmarcou/IGoR/

C++ software designed to infer V(D)J recombination related processes from sequencing data.

Proper citation: IGoR (RRID:SCR_024053) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/paulklemm_PHD/proteinortho

Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis.

Proper citation: Proteinortho (RRID:SCR_024177) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/genomicepidemiology/kmerresistance/src/master/

Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.

Proper citation: KmerResistance (RRID:SCR_024058) Copy   

•   Source: SciCrunch Registry

http://proda.stanford.edu/

Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures.

Proper citation: ProDA (RRID:SCR_024171) Copy   

•   Source: SciCrunch Registry

https://github.com/klebgenomics/Kleborate

Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive.

Proper citation: Kleborate (RRID:SCR_024051) Copy   

•   Source: SciCrunch Registry

http://www.swisstargetprediction.ch/

Web tool to estimate the most probable macromolecular targets of small molecule, assumed as bioactive. Prediction is founded on combination of 2D and 3D similarity with library of known actives on proteins from three different species.

Proper citation: SwissTargetPrediction (RRID:SCR_023756) Copy   

•   Source: SciCrunch Registry

https://ukoethe.github.io/vigra/

Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework.

Proper citation: VIGRA (RRID:SCR_024100) Copy   

•   Source: SciCrunch Registry