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https://shimadzu.com.au/labsolutions

Software package for data analysis by Shimadzu Oceania.

Proper citation: LabSolutions (RRID:SCR_018241) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/cancer/cga/polysolver

Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.

Proper citation: Polysolver (RRID:SCR_022278) Copy   

•   Source: SciCrunch Registry

https://github.com/mrcgndr/plant_cataloging_workflow

Software workflow for automatized spatio temporal plant positioning based on UAV images.

Proper citation: Plant Cataloging Workflow (RRID:SCR_022276) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/sigcom-lincs

Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.

Proper citation: SigCom LINCS (RRID:SCR_022275) Copy   

•   Source: SciCrunch Registry

http://kinefold.curie.fr/

Web service for RNA/DNA folding predictions including pseudoknots and entangled helices.Used for prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

Proper citation: KineFold (RRID:SCR_022273) Copy   

•   Source: SciCrunch Registry

https://www2.hhu.de/rna/html/hexplorer_score.php

Web tool for genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Allows landscaping of splicing regulatory regions, provides quantitative measure of mutation effects on splice enhancing and silencing properties and permitts calculation of mutationally most effective nucleotide.

Proper citation: HEXplorer score (RRID:SCR_022269) Copy   

•   Source: SciCrunch Registry

http://www.codons.org/calc.html

Software tool for calculating and comparing synonymous codon usage and its impact on protein folding. Used to harmonize codon usage frequencies for heterologous gene expression. Codon usage calculator that evaluates relative usage frequencies of synonymous codons used to encode protein sequence of interest and compares these results to rigorous null mode.Evaluates synonymous codon usage patterns for any coding sequence from any fully sequenced genome.

Proper citation: %MinMax (RRID:SCR_022268) Copy   

•   Source: SciCrunch Registry

https://github.com/slimsuite/diploidocus

Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly.

Proper citation: Diploidocus (RRID:SCR_021231) Copy   

•   Source: SciCrunch Registry

https://jump-cellpainting.broadinstitute.org

Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes.

Proper citation: JUMP Cell Painting Consortium (RRID:SCR_021868) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/gernerlab/cytomap/-/wikis/home

Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.

Proper citation: CytoMAP (RRID:SCR_021227) Copy   

•   Source: SciCrunch Registry

https://github.com/FRED-2/OptiType

Software tool for precision HLA typing from next generation sequencing data.

Proper citation: OptiType (RRID:SCR_022279) Copy   

•   Source: SciCrunch Registry

http://nf.synapse.org

Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases.

Proper citation: NF Data Portal (RRID:SCR_021683) Copy   

•   Source: SciCrunch Registry

https://github.com/B-UMMI/LMAS

Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored.

Proper citation: LMAS (RRID:SCR_022251) 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

http://sanger-pathogens.github.io/snp-sites/

Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis.

Proper citation: SNP-sites (RRID:SCR_022265) Copy   

•   Source: SciCrunch Registry

https://github.com/dfguan/purge_dups

Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.

Proper citation: purge dups (RRID:SCR_021173) Copy   

•   Source: SciCrunch Registry

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

Software package for MATLAB that makes motion correction, segmentation, signal extraction and dimension reduction, analysis, and visualization of calcium imaging data easy to implement. Open source toolbox for analysis of calcium imaging data.

Proper citation: EZcalcium (RRID:SCR_022354) Copy   

•   Source: SciCrunch Registry

https://pasquali-lab.gitlab.io/umi4cats/

Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C.

Proper citation: UMI4Cats (RRID:SCR_021780) Copy   

•   Source: SciCrunch Registry

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

Software Python toolbox that makes fiber photometry data analysis intuitive and light on programming.Used to measure neural activity of freely behaving animals.

Proper citation: GuPPy (RRID:SCR_022353) Copy   

•   Source: SciCrunch Registry

https://github.com/sgoldenlab/simba

Open source software toolkit for computer classification of complex social behaviors in experimental animals.

Proper citation: Simple Behavior Analysis (RRID:SCR_021413) Copy   

•   Source: SciCrunch Registry