Tools   Select Another Resource Report Type

https://github.com/AllenInstitute/scrattch.hicat

Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute.

Proper citation: Scrattch.Hicat (RRID:SCR_018099) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.com/biomerieux-data-science/clustlasso

Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.

Proper citation: clustLasso (RRID:SCR_018820) Copy   

•   Source: SciCrunch Registry
  

https://github.com/quest-bih/oddpub

Text mining algorithm to screen biomedical publications to find data sharing statements. Algorithm that parses set of publications and detects which publications disseminated Open Data or Open Code together with publication. Tailored towards biomedical literature.

Proper citation: ODDPub (RRID:SCR_018385) Copy   

•   Source: SciCrunch Registry
  

https://github.com/alleninstitute/cocoframer

Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer.

Proper citation: Cocoframer (RRID:SCR_023817) Copy   

•   Source: SciCrunch Registry
  

https://www.pathogens.se

Portal provides information, guidelines, data, services, and other resources aimed at supporting Swedish research community to share data related to pathogens and pandemic preparedness.

Proper citation: Swedish Pathogens Portal (RRID:SCR_024866) Copy   

•   Source: SciCrunch Registry
  

https://www.census.gov/quickfacts/fact/table/AL,MD,MO,CT/PST045223

Data about Alabama, Maryland, Missouri and Connecticut people and economy.

Proper citation: 2023 U.S. Census Quick Facts about Alabama, Maryland, Missouri and Connecticut (RRID:SCR_025902) Copy   

•   Source: SciCrunch Registry
  

https://www.bioinformatics.com.cn/SRplot

Web server that integrated data visualization and graphing functions together. Can be run easily with all Web browsers, with user-friendly graphical interface, users can paste your data directly into input box according to defined file format. Resulting graphs can be downloaded in bitmap (PNG or TIFF) or vector (PDF or SVG) format in publication quality. Used for data visualization and graphing.

Proper citation: SRplot (RRID:SCR_025904) Copy   

•   Source: SciCrunch Registry
  

https://www.statista.com/

Platform for data and statistics. Website provides data-driven services, collection of statistics, reports, and insights on over 80,000 topics.

Proper citation: statista (RRID:SCR_026121) Copy   

•   Source: SciCrunch Registry
  

https://www.mammaldiversity.org/

Updatable online database of mammal taxonomic and biodiversity information hosted by American Society of Mammalogists. Provides information on species-level and higher taxonomic changes, thereby promoting more rigorous study of mammalian biodiversity worldwide. The initial objective has been to aggregate, curate, and compile, new citations on species descriptions and taxonomic revisions into regular releases that are downloadable in comma-delimited format. Downstream goals include expanded hosting of ecological, trait, and taxonomic data.

Proper citation: Mammal Diversity Database (RRID:SCR_026173) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/DDRTree/index.html

Software R package provides implementation of framework of reversed graph embedding which projects data into reduced dimensional space while constructs principal tree which passes through middle of data simultaneously.

Proper citation: DDRTree (RRID:SCR_026795) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nf-core/rnaseq

Software RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. Can be used to analyse RNA sequencing data obtained from organisms with reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix QC report.

Proper citation: rnaseq (RRID:SCR_026973) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/plyr/index.html

Software R package for splitting, applying and combining data. Used to split up big data structure into homogeneous pieces, apply function to each piece and then combine all the results back together.

Proper citation: plyr (RRID:SCR_026985) Copy   

•   Source: SciCrunch Registry
  

https://cnmdp.atlassian.net/wiki/spaces/CNMDP/overview

Platform to store, analyze, and share large amounts of various types of data to facilitate research, and ultimately, unravel the complex connections between the brain and the heart.

Proper citation: Cardio-Neuro-Mind Data Platform (RRID:SCR_027008) Copy   

•   Source: SciCrunch Registry
  

https://www.cultivarium.org/

Cultivarium creates tools for life scientists to expand access to novel microorganisms, inspire new research avenues, and push the frontiers of biotechnology. Aggregates information, data, and publications for bacteria, fungi, archaea, and protists.

Proper citation: Cultivarium (RRID:SCR_027163) Copy   

•   Source: SciCrunch Registry
  

https://nanda.isr.umich.edu/

Open data repository to facilitate research on the relationship between neighborhoods and health, especially within the context of large federally funded surveys and cohort studies. Used to explore topics of interest to neighborhoods and communities. NaNDA measures can be readily linked to survey data, cohort studies, electronic medical records, or other microdata, via geographic identifiers, or combined and explored on their own. NaNDA datasets are created by researchers in the Social Environment and Health program at the University of Michigan Institute for Social Research.

Proper citation: National Neighborhood Data Archive (RRID:SCR_027451) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/trackViewer.html

Software R package to visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Proper citation: trackViewer (RRID:SCR_027743) Copy   

•   Source: SciCrunch Registry
  

https://community.researchspace.com

Electronic Lab Notebook digital platform designed to help researchers organize, store, and share experimental notes, protocols, and data. Acting as a modern replacement for traditional paper lab notebooks, it operates as an institution-wide research data management (RDM) system.

Proper citation: RSpace ELN (RRID:SCR_028561) Copy   

•   Source: SciCrunch Registry