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https://www.nitrc.org/projects/qcalign
Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas.
Proper citation: QCAlign (RRID:SCR_023088) Copy
Joint computational research center with Carnegie Mellon University and University of Pittsburgh. Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research.
Proper citation: Pittsburgh Supercomputing Center (RRID:SCR_022823) Copy
https://github.com/vesselman/SparkAn
Software tool for custom calcium imaging analysis.
Proper citation: SparkAn (RRID:SCR_022028) Copy
https://rewireneuro.com/product/pipsqueak/
Software image analysis tool as older ImageJ/Fiji plugin version.
Proper citation: Pipsqueak AI (RRID:SCR_022149) Copy
http://colibread.inria.fr/software/mapsembler2/
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Proper citation: Mapsembler2 (RRID:SCR_024102) Copy
https://github.com/gerddie/maxflow
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Proper citation: MAXFLOW (RRID:SCR_024103) Copy
Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell.
Proper citation: Smart-seq2 Single Sample Pipeline (RRID:SCR_021228) Copy
Collection as result of joint work of scientists, technicians and students from Federal University of Rio de Janeiro and Technical-Scientific Association Paul Ehrlich. Center of reference and excellence in cell culture in Brazil and in our continent. Collection of human and animal cells that operates as service provider in Brazil and is the largest in South America.
Proper citation: Rio de Janeiro Cell Bank (RRID:SCR_023181) Copy
https://catalog.bcrc.firdi.org.tw/
Systematic and service oriented BioResource Center in Asia. Member of World Federation for Culture Collections from 1984 until now. BCRC is the first BRC certified by international organization of ISO quality system. Approved by Taiwan Biodiversity Information Facility.
Proper citation: Taiwan Bioresource Collection and Research Center (RRID:SCR_023180) Copy
https://cellbank.nibiohn.go.jp/english/
Collection of various human and animal culture cells including cancer and genetically modified cells. Cell resources are distributed to researchers across Japan and around the world. These cells are comprehensively qualified by testing microbial contamination, virus contamination and cross culture contamination. Some cells are characterized by karyotyping and/or cell surface markers. In collaboration with other major cell banks in the world, we are developing methods for cell culturing and quality control in order to support fundamental research on medical of pharmaceutical sciences.
Proper citation: Japanese Collection of Research Bioresources Cell Bank (RRID:SCR_023187) Copy
Software pipeline for single-nucleus RNAseq data generated by Smart-seq2 assays.Used to simultaneously process multiple libraries of single nuclei Smart-seq2 and Smart-seq4 data. For each library (nucleus), the pipeline trims paired FASTQ files, aligns trimmed reads to the genome, counts intronic and exonic reads, and calculates quality control metrics. Counts and metrics for all libraries are combined into merged Loom formatted count matrix.
Proper citation: Smart-seq2 Single Nucleus Multi Sample Pipeline (RRID:SCR_021312) Copy
https://github.com/ENCODE-DCC/chip-seq-pipeline2/
Software tool as ChIP-seq pipeline for processing ChIP-seq reads, aligning to reference genome, peak calling, and IDR analysis of replicate data according to ENCODE standards.
Proper citation: ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (RRID:SCR_021323) Copy
https://www.ncbi.nlm.nih.gov/books/NBK179288/
Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.
Proper citation: Entrez Direct (RRID:SCR_024136) Copy
https://doua.prabi.fr/software/njplot
Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Proper citation: NJplot (RRID:SCR_024137) Copy
https://www.syngene.com/software/genetools-automatic-image-analysis/
Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.
Proper citation: GeneTools (RRID:SCR_022505) Copy
Center coordinates ideas and investments to advance and democratize access to Stanford cores, instrumentation, scientific and technical staff, allowing users to perform innovative, rigorous experiments.
Proper citation: Stanford University Community of Shared Advanced Research Platforms (RRID:SCR_022986) Copy
https://github.com/wdecoster/NanoPlot
Software package as plotting tool for long read sequencing data and alignments.
Proper citation: NanoPlot (RRID:SCR_024128) Copy
https://pypi.org/project/OBITools/
Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.
Proper citation: OBITools (RRID:SCR_024141) Copy
https://freeimage.sourceforge.io/
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Proper citation: FreeImage (RRID:SCR_024022) Copy
GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.
Proper citation: GDCM (RRID:SCR_024027) Copy
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