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https://github.com/ncbi/SRPRISM/
Software tool as single read paired read indel substitution minimizer.
Proper citation: Single Read Paired Read Indel Substitution Minimizer (RRID:SCR_018023) Copy
https://github.com/rrwick/Porechop
Software tool for finding and removing adapters from Oxford Nanopore reads.
Proper citation: Porechop (RRID:SCR_016967) Copy
https://github.com/nipy/heudiconv
Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts.
Proper citation: HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) Copy
http://glmmadmb.r-forge.r-project.org/
Software R package for fitting generalized linear mixed models (GLMMs) using AD Model Builder. Fits mixed-effects models to count data using Poisson or negative binomial response distributions.
Proper citation: glmmADMB (RRID:SCR_016859) Copy
https://github.com/lufuhao/ATACseqMappingPipeline
Software tool as pipeline to map ATAC-seq data to large genome, for example, for wheat. It splits large genome files into parts and do mapping and then finally merge them.
Proper citation: ATACseqMappingPipeline (RRID:SCR_017558) Copy
http://younglab.wi.mit.edu/super_enhancer_code.html
To create stitched enhancers, and to separate super enhancers from typical enhancers using sequencing data given file of previously identified constituent enhancers .
Proper citation: ROSE (RRID:SCR_017390) Copy
https://github.com/bjohnnyd/fs-tool
Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes.
Proper citation: fs-tool (RRID:SCR_018250) Copy
https://broadinstitute.github.io/warp/docs/Pipelines/Single_Cell_ATAC_Seq_Pipeline/README
Pipeline developed in collaboration with Bing Ren lab and supports processing of BICCN single-cell/nucleus ATAC-seq datasets. Pipeline uses python module SnapTools to align and process paired reads in form of FASTQ files. Produces hdf5-structured Snap file that includes cell-by-bin count matrix. Final outputs also include GA4GH compliant aligned BAM and QC metrics.
Proper citation: scATAC Pipeline (RRID:SCR_018919) Copy
Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science.
Proper citation: EarthCube (RRID:SCR_024576) Copy
https://github.com/ABCD-STUDY/redcap-hook-framework
Software tool to organize and deploy custom hooks in a single project or across the entire instance. It features multi-language support for data entry and survey pages, a bar-code for text fields, and highlighting of rows on data entry and survey pages that have been filled out.
Proper citation: redcap-hook-framework (RRID:SCR_016028) Copy
https://metagenote.niaid.nih.gov/
Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.
Proper citation: METAGENOTE (RRID:SCR_018494) Copy
https://med.stanford.edu/starr-tools.html
Platform developed and operated by Stanford Medicine Research IT team for working with clinical data for research purposes. Permits collection and aggregation of all clinical data generated at Stanford for care purposes, and articulates formal approval process each research project must follow in order to obtain and work with this data for research purpose. Home of stride/web tools for Cohort Discovery and Chart Review.
Proper citation: Stanford Medicine Research Data Repository (RRID:SCR_018686) Copy
http://www.statsoft.com/Products/STATISTICA/Product-Index
Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures.
Proper citation: STATISTICA (RRID:SCR_014213) Copy
https://cibersort.stanford.edu/
Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.
Proper citation: CIBERSORT (RRID:SCR_016955) Copy
https://github.com/sccn/labstreaminglayer
System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording.
Proper citation: Lab Streaming Layer (RRID:SCR_017631) Copy
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
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
Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.
Proper citation: HED Tags (RRID:SCR_014074) Copy
https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.
Proper citation: Skyline (RRID:SCR_014080) Copy
http://www.originlab.com/index.aspx?go=PRODUCTS/Origin
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.
Proper citation: Origin (RRID:SCR_014212) Copy
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