Tools   Select Another Resource Report Type

https://software.broadinstitute.org/morpheus/

Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.

Proper citation: Morpheus by Broad Institute (RRID:SCR_017386) Copy   

•   Source: SciCrunch Registry
  

https://brainreader.net

Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.

Proper citation: Brainreader (RRID:SCR_017308) Copy   

•   Source: SciCrunch Registry
  

http://pcddb.cryst.bbk.ac.uk/home.php

Public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. For authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. Includes links for each entry to bioinformatics databases. Data are freely available to accessors either as single files or as complete data bank downloads.

Proper citation: Protein Circular Dichroism Data Bank (PCDDB) (RRID:SCR_017428) Copy   

•   Source: SciCrunch Registry
  

https://www.ibis-network.org/index.html

Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers

Proper citation: IBIS Network (RRID:SCR_017399) Copy   

•   Source: SciCrunch Registry
  

https://ldlink.nci.nih.gov/?tab=ldmatrix

Software tool to create interactive heatmap matrix of pairwise linkage disequilibrium statistics.

Proper citation: LDMatrix (RRID:SCR_017391) Copy   

•   Source: SciCrunch Registry
  

https://www.qiagenbioinformatics.com/products/clc-genomics-server/

Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler.

Proper citation: CLC Genomics Server (RRID:SCR_017396) Copy   

•   Source: SciCrunch Registry
  

https://www.daqcord.org/

Software tool for practical self assessment and reporting method for clinical research studies, to capture key information about data acquisition and quality control measures. Linked to dataset so that potential research collaborators can determine if data meets their needs and expectations.

Proper citation: DAQCORD (RRID:SCR_017395) Copy   

•   Source: SciCrunch Registry
  

https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater

Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses.

Proper citation: Galaxy scater (RRID:SCR_017394) 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://pathology.med.upenn.edu/research/core-resources/tumor-tissue-biospecimen-bank

Centralized biorepository of human biosamples. TTAB is responsible for the collection, processing, and storage of human blood, fluid, and tissue at the University of Pennsylvania Health System. TTAB has a collection bench within Surgical Pathology Suite at Hospital of University of Pennsylvania (HUP).� Our collection bench sits adjacent to frozen section teams managing clinical sample collection and allowing for tight integration of tissue sample collection with clinical pathology teams.

Proper citation: University of Pennsylvania Perelman School of Medicine Tumor Tissue Biospecimen Bank Core Facility (RRID:SCR_022430) 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
  

http://hub.docker.com/r/marchalc/hicres/

Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution.

Proper citation: HiCRes (RRID:SCR_022319) 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
  

https://www.med.upenn.edu/ifi/cytofservicecenter.html

CyTOF�enables multi-parametric high-dimensional single�cell analysis�of more than 40 markers per cell, with�minimal background and compensation�issues.�Core�offers variety of�CyTOF-related services including�reagent distribution, consultation,�antibody conjugation, and data acquisition.�

Proper citation: University of Pennsylvania Perelman School of Medicine IFI CyTOF Service Center Core Facility (RRID:SCR_022410) 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://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