Tools   Select Another Resource Report Type

https://pm4ngs.readthedocs.io/

Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.

Proper citation: PM4NGS (RRID:SCR_019164) Copy   

•   Source: SciCrunch Registry

https://github.com/gtonkinhill/panaroo

Software pipeline for pangenome investigation. Shares information between genomes to correct errors. Can call large structural variants.Fast and scalable to over 10k bacterial genomes.

Proper citation: Panaroo (RRID:SCR_021090) Copy   

•   Source: SciCrunch Registry

https://www.creative-peptides.com/services/formulation-development.html

Service to determine optimal dosage form, composition and manufacturing route for pharmaceutical products.

Proper citation: Creative Peptides: Formulation Development Service Resource (RRID:SCR_022223) Copy   

•   Source: SciCrunch Registry

https://www.creative-peptides.com/services/peptide-lead-optimization.html

Provides optimized one stop solution for peptide lead drugs. Used to improve upon lead molecule that demonstrates activity at target of interest by optimizing its potency or selectivity at target and its absorption, distribution, metabolism and elimination properties.

Proper citation: Creative Peptides: Peptide Lead Optimization Service Resource (RRID:SCR_022222) Copy   

•   Source: SciCrunch Registry

https://www.creative-peptides.com/services/peptide-drug-bioconjugations.html

Custom peptide synthesis, modification, and conjugation services involve chemical modification of peptide at highly specific sites. This allows for attachment of drugs or bioactive molecules though variety of coupling techniques.

Proper citation: Creative Peptides Peptide Drug Bioconjugations Service Resource (RRID:SCR_022221) Copy   

•   Source: SciCrunch Registry

https://github.com/Benson-Genomics-Lab/TRF

Software tool to locate and display tandem repeats in DNA sequences. Used to analyze DNA sequences.

Proper citation: Tandem Repeats Finder (RRID:SCR_022065) Copy   

•   Source: SciCrunch Registry

http://neomorph.salk.edu/omb/

Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type.

Proper citation: Brain Cell Methylation Viewer (RRID:SCR_020954) Copy   

•   Source: SciCrunch Registry

https://www.creative-peptides.com/services/total-peptide-library-construction-technology.html

Service uses bioinformatics methods to compress peptide information, which can integrate information of multiple peptide into one peptide. Provides collection of small peptide of specific length and different sequences, which includes permutation and combination of various amino acid sequences in short peptide of this length.Total peptide library for new drug research and development.

Proper citation: Creative Peptides Total Peptide Library Construction Service Resource (RRID:SCR_022219) Copy   

•   Source: SciCrunch Registry

https://mass-spec.stanford.edu/instruments

System includes SQD2 as single quadrupole MS with Waters H-Class Acquity UPLC, operated as open access platform for trained users. SQ Detector2 is single quadrupole mass detector for chromatography compatible with range of chromatography platforms and ionization sources.

Proper citation: Waters: SQD2 LC/MS system (RRID:SCR_022217) Copy   

•   Source: SciCrunch Registry

http://old.protein.bio.unipd.it/cspritz/

Web tool for prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.

Proper citation: CSpritz (RRID:SCR_021884) Copy   

•   Source: SciCrunch Registry

http://redrocksw.com/

Software tool for statistics and data visualization by Red Rock Software, Inc. Provides unparalleled chart selection, data analysis and graph customization capabilities.

Proper citation: Deltagraph (RRID:SCR_018084) Copy   

•   Source: SciCrunch Registry

https://swissmodel.expasy.org/

Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists.

Proper citation: SWISS-MODEL (RRID:SCR_018123) Copy   

•   Source: SciCrunch Registry

https://signor.uniroma2.it/

Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.

Proper citation: SIGNOR (RRID:SCR_018485) Copy   

•   Source: SciCrunch Registry

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://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