Tools   Select Another Resource Report Type

https://github.com/STOmics/BatchEval

Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report.

Proper citation: BatchEval (RRID:SCR_024546) Copy   

•   Source: SciCrunch Registry

https://science.bostongene.com/kassandra/

Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression.

Proper citation: Kassandra (RRID:SCR_024548) Copy   

•   Source: SciCrunch Registry

https://covid-19.ensembl.org/

Ensembl SARS-Cov2 data portal.

Proper citation: Ensembl Covid-19 (RRID:SCR_024704) Copy   

•   Source: SciCrunch Registry

https://github.com/cchandre/Polarimetry

Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples.

Proper citation: PyPOLAR (RRID:SCR_024681) Copy   

•   Source: SciCrunch Registry

https://github.com/katiasmirn/PERFect#perfect-permutation-filtering-package-in-r

Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

Proper citation: PERFect (RRID:SCR_024682) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/csr/1975_2016/

Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States.

Proper citation: NCI SEER Cancer Statistics Review (RRID:SCR_024685) Copy   

•   Source: SciCrunch Registry

http://oppnet.nih.gov/

OppNet is a trans-NIH initiative to expand the agency's funding of basic behavioral and social sciences research (b-BSSR). Basic-BSSR studies mechanisms and processes that influence behavior at the individual, group, community and population level. Research results lead to new approaches for reducing risky behaviors and improving the adoption of healthy practices. The mission of OppNet is to pursue opportunities for strengthening basic behavioral and social science research (b-BSSR) at the NIH while innovating beyond existing investments. * OppNet advances basic behavioral and social science research through activities and initiatives that build a body of knowledge about the nature of behavior and social systems. * OppNet prioritizes activities and initiatives that focus on basic mechanisms of behavior and social processes; that are relevant to the missions and public health challenges of multiple NIH Institutes, Centers and Offices (ICOs); and that build upon existing NIH investments without replicating them. All NIH Institutes and Centers (ICs) share the mission of supporting b-BSSR. OppNet will also develop a plan for focused multi-year programs across ICs to advance priority topics within b-BSSR.

Proper citation: OppNet - Basic Behavioral and Social Science Opportunity Network (RRID:SCR_003522) Copy   

•   Source: SciCrunch Registry

https://ganjoho.jp/public/index.html

Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information.

Proper citation: Cancer Information Service (RRID:SCR_024445) Copy   

•   Source: SciCrunch Registry

https://www.sfwmd.gov/our-work/cerp-project-planning

Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government.

Proper citation: Comprehensive Everglades Restoration Plan (RRID:SCR_024557) Copy   

•   Source: SciCrunch Registry

https://github.com/torognes/vsearch

Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data.

Proper citation: VSEARCH (RRID:SCR_024494) Copy   

•   Source: SciCrunch Registry

https://www.tomocube.com/product/tomostudio/

Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data.

Proper citation: TomoStudio (RRID:SCR_024498) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/spliceai/

Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants.

Proper citation: Splice AI (RRID:SCR_024532) Copy   

•   Source: SciCrunch Registry

https://www.photometrics.com/products/ocular

Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

Proper citation: Ocular (RRID:SCR_024490) Copy   

•   Source: SciCrunch Registry

https://github.com/SharonLutz/Umediation

Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding.

Proper citation: Umediation (RRID:SCR_024492) Copy   

•   Source: SciCrunch Registry

https://github.com/bkntr/brainways

Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices.

Proper citation: Brainways (RRID:SCR_024402) Copy   

•   Source: SciCrunch Registry

https://www.reading.ac.uk/bioinf/IntFOLD/

Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences.

Proper citation: IntFOLD (RRID:SCR_024523) Copy   

•   Source: SciCrunch Registry

http://rnainformatics.org.cn/RiboToolkit/

Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs.

Proper citation: RiboToolkit (RRID:SCR_024406) Copy   

•   Source: SciCrunch Registry

https://github.com/sina-cb/Tn-seqExplorer

Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.

Proper citation: Tn-seq explorer (RRID:SCR_024387) Copy   

•   Source: SciCrunch Registry

https://github.com/PyWavelets/pywt

Software Python package for wavelet analysis.

Proper citation: PyWavelets (RRID:SCR_024421) Copy   

•   Source: SciCrunch Registry

http://saclab.tamu.edu/essentiality/transit/

Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.

Proper citation: TRANSIT (RRID:SCR_024389) Copy   

•   Source: SciCrunch Registry