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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
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://www.lungepigenome.org/
Project to provide data on genome and epigenome of human lung to facilitate research efforts of investigators studying diseases of lung including COVID-19.Collaboration among multiple groups at University of California including Center for Epigenomics, Gaulton lab and Sun lab at UCSD Department of Pediatrics. This work is conducted as part of LungMAP consortitum.
Proper citation: Lung Genome Browser (RRID:SCR_019255) 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
Data integration and dissemination project for carbohydrate and glycoconjugate related data. Computational and informatics resources for glycoscience. Portal provides user-friendly interface that facilitates exploration of glycoscience data from diverse international bioinformatics resources, including National Center for Biotechnology Information (NCBI), UniProt, Protein Data Bank (PDB), UniCarbKB, and GlyTouCan glycan structure repository. Retrieves information from data sources and integrates and harmonizes this data. Includes knowledge about molecular, biophysical and functional properties of glycans, genes, proteins and lipids organized in pathways and ontologies, plus data related to mutation and expression.
Proper citation: GlyGen (RRID:SCR_023438) Copy
http://www.bioconductor.org/packages/2.12/bioc/html/PICS.html
R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.
Proper citation: PICS (RRID:SCR_001093) Copy
Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.
Proper citation: ImageJ (RRID:SCR_003070) Copy
http://www.type2diabetesgenetics.org/
Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.
Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.
Proper citation: BioMart Project (RRID:SCR_002987) Copy
https://www.phantomhighspeed.com/resourcesandsupport/phantomresources/pccsoftware
Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems.
Proper citation: Phantom Camera Control (RRID:SCR_021080) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) Copy
Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification.
Proper citation: MetaboAnalyst (RRID:SCR_015539) Copy
Open source project to harness scientific and public health potential of pathogen genome data. Provides continually updated view of publicly available data alongside powerful analytic and visualization tools for use by community. Used to aid epidemiological understanding and improve outbreak response. Open source SARS-CoV-2 genome data and analytic and visualization tools.
Proper citation: Nextstrain (RRID:SCR_018223) Copy
https://github.com/AllenInstitute/AllenSDK
Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas.
Proper citation: Allen Software Development Kit (RRID:SCR_018183) Copy
http://www.cbs.dtu.dk/services/NetMHCpan/
Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy
http://www.imgt.org/IMGTrepertoire/
Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system.
Proper citation: IMGT Repertoire (RRID:SCR_018220) Copy
Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R.
Proper citation: Velocyto (RRID:SCR_018167) Copy
https://github.com/astroML/astroML
Software Python package for machine learning, statistics and data mining. Contains library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical data sets, and examples of analyzing and visualizing astronomical data sets. Repository of common tools and routines used for statistical data analysis in astronomy and astrophysics.
Proper citation: astroML (RRID:SCR_018138) Copy
https://github.com/r3fang/SnapTools
Software tool as module for working with snap files in Python. Snap files are designed for storing single nucleus ATAC-seq datasets.
Proper citation: SnapTools (RRID:SCR_018097) Copy
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