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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/holab-hku/Vulture
Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain.
Proper citation: Vulture (RRID:SCR_024720) Copy
Software finite element analysis package. Used to solve field problems.
Proper citation: CalculiX (RRID:SCR_024771) Copy
https://www.tidyverse.org/blog/2018/11/parsnip-0-0-1/
Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc.
Proper citation: Parsnip (RRID:SCR_024744) Copy
Software visualization grammar and GPU-accelerated toolkit for genomic data. Visualization grammar and GPU-accelerated rendering engine for genomic data. Grammar based toolkit for authoring tailored, interactive visualizations for genomic data analysis.
Proper citation: GenomeSpy (RRID:SCR_024837) Copy
https://github.com/bioinform/somaticseq
Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification.
Proper citation: SomaticSeq (RRID:SCR_024891) Copy
https://bioconductor.org/packages/combi/
Software R package for simultaneous exploration of multiple datasets. Compositional omics model based visual integration.Used to integrate omics data for visualization, with special focus on compositionality.
Proper citation: combi (RRID:SCR_024986) Copy
https://cran.r-project.org/web/packages/table1/
Software R package to create HTML tables of descriptive statistics, as one would expect to see as the first table in medical epidemiological journal article. Used for generating tables of descriptive statistics in HTML.
Proper citation: table1 (RRID:SCR_024900) Copy
Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia.
Proper citation: Daphnia Atlas (RRID:SCR_024913) Copy
https://github.com/xinhe-lab/GSFA
Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.
Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy
https://www.rdocumentation.org/packages/gplots/versions/3.1.3.1
Software R package to create figures.
Proper citation: gplots (RRID:SCR_025035) Copy
https://CRAN.R-project.org/package=nricens
Software R package for calculating Net Reclassification Improvement for risk prediction models with time to event and binary data. NRI for risk prediction models with time to event and binary response data.
Proper citation: nricens (RRID:SCR_025138) Copy
https://CRAN.R-project.org/package=ggsurvfit
Software R package for flexible time-to-event figures creation. Used to create figures ready for publication.
Proper citation: ggsurvfit (RRID:SCR_025045) Copy
https://CRAN.R-project.org/package=gridExtra
Softwate R package to work with "grid" graphics, notably to arrange multiple grid-based plots on page, and draw tables. Miscellaneous functions for Grid graphics.
Proper citation: gridExtra (RRID:SCR_025249) Copy
https://lambada.icm-institute.org
Reference atlas of the developing post-natal mouse brain. Provides data and annotations on distribution of cells and gene expression in mouse brain.
Proper citation: LAMBADA (RRID:SCR_025382) Copy
https://github.com/ingmarboeschen/JATSdecoder
Software metadata and text extraction and text manipulation tool set for statistical programming language R. Facilitates text mining projects on scientific articles in 'NISO-JATS' format by enabling individual selection of metadata and text parts.
Proper citation: JATSdecoder (RRID:SCR_025279) Copy
https://github.com/MannLabs/pydiaid
Software Python package for DIA with automated isolation design. Used for Data-Independent Acquisition providing Automated Isolation Design. Optimally generates dia-PASEF and synchro-PASEF methods and places them optimally within the m/z – ion mobility (IM) plane.
Proper citation: py_diAID (RRID:SCR_025304) Copy
https://search.kg.ebrains.eu/?category=Project#904b7981-0c68-4af6-b3bb-3d9a648b3a7c
Continuous 3D reference atlas for postnatal mouse brain.
Proper citation: Developmental Mouse Brain atlas (RRID:SCR_025324) Copy
https://pvactools.readthedocs.io/en/latest/
Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design.
Proper citation: pVACtools (RRID:SCR_025435) Copy
https://CRAN.R-project.org/package=aod
Software R package to analyse overdispersed counts or proportions.
Proper citation: aod: Analysis of Overdispersed Data (RRID:SCR_025516) Copy
Organization that works with knowledge professionals to create, support and deliver programs, services and technologies that allow for equitable access to world knowledge and cultural heritage. Hosts data-migration, content licensing, and community supported software programs for libraries, archives, museums and research organizations worldwide.
Proper citation: Lyrasis (RRID:SCR_025403) Copy
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