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https://github.com/HicServices/DicomTypeTranslation
Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database.
Proper citation: DicomTypeTranslator (RRID:SCR_018878) Copy
https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data.
Proper citation: RiboTaper (RRID:SCR_018880) Copy
https://github.com/BNadel/GEDIT
Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices.
Proper citation: GEDIT (RRID:SCR_019277) Copy
https://bitbucket.org/berkeleylab/metabat/src/master/
Software statistical framework for reconstructing genomes from metagenome data. Open source software tool for accurately reconstructing single genomes from complex microbial communities.
Proper citation: MetaBAT (RRID:SCR_019134) Copy
https://github.com/constantAmateur/SoupX
Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data.
Proper citation: SoupX (RRID:SCR_019193) Copy
https://github.com/statOmics/tradeSeq
Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data.
Proper citation: tradeSeq (RRID:SCR_019238) Copy
http://bioinformatics.sdstate.edu/go/
Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks.
Proper citation: ShinyGO (RRID:SCR_019213) Copy
https://bioconductor.org/packages/biomaRt/
Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis.
Proper citation: biomaRt (RRID:SCR_019214) Copy
https://github.com/ShaokunAn/D-EE
Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup.
Proper citation: D-EE (RRID:SCR_019058) Copy
https://bioconductor.org/packages/ReactomePA/
Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.
Proper citation: ReactomePA (RRID:SCR_019316) Copy
Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.
Proper citation: ImJoy (RRID:SCR_020935) Copy
Software tool for phylogenomic inference.
Proper citation: IQ TREE (RRID:SCR_021163) Copy
http://srna-workbench.cmp.uea.ac.uk
Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.
Proper citation: UEA sRNA Workbench (RRID:SCR_020947) Copy
Software tool as next generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.Enables researchers to start analysis with raw DNA sequence data and finish with publication quality figures and statistical results. Used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities.
Proper citation: QIIME2 (RRID:SCR_021258) Copy
https://github.com/nanoporetech/tombo
Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal.
Proper citation: Tombo (RRID:SCR_024388) Copy
Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.
Proper citation: Assemblytics (RRID:SCR_023967) Copy
https://zhanggroup.org/NW-align/
Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.
Proper citation: NW-align (RRID:SCR_024138) Copy
https://sourceforge.net/projects/microbegps/
Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.
Proper citation: MicrobeGPS (RRID:SCR_024112) Copy
https://pyscanfcs.readthedocs.io/en/stable/
Software application for perpendicular line scanning fluorescence correlation spectroscopy.
Proper citation: pyscanfcs (RRID:SCR_024190) Copy
https://github.com/pyranges/pyranges
Software application for efficient comparison of genomic intervals in Python.
Proper citation: pyranges (RRID:SCR_024191) Copy
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