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https://www.gnu.org/software/grep/manual/grep.html
Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options.
Proper citation: GNU Grep (RRID:SCR_018212) Copy
https://usa.jpk.com/news/2011/directoverlay-display-analysis-software-from-jpk-instruments
Software package for display of light microscopy images together with atomic force microscopy images.
Proper citation: DirectOverlay (RRID:SCR_018978) 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
https://github.com/a-h-b/dadasnake
Software tool as snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology.
Proper citation: dadasnake (RRID:SCR_019149) Copy
https://www.gnu.org/software/tar/
Software tool to create tar archives, as well as various other kinds of manipulation. Used to extract files, to store additional files, or to update or list files which were already stored. Can direct its output to available devices, files, or other programs, can access remote devices or files.
Proper citation: GNU Tar (RRID:SCR_018216) Copy
https://www.gnu.org/software/gawk/manual/gawk.html
Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors.
Proper citation: GNU Awk (RRID:SCR_018211) Copy
https://github.com/Kingsford-Group/kourami
Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.
Proper citation: Kourami (RRID:SCR_022280) 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
https://github.com/mourisl/Rascaf
Software tool for scaffolding with RNA-seq read alignments. Used for improving genome assembly with RNA sequencing data.
Proper citation: Rascaf (RRID:SCR_022014) Copy
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005095
Software tool to describe spatial patterns in degrees of inhomogeneity and to incorporate intensity based correction to analyze images with wide range of resolutions. Can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at cell surface.
Proper citation: QuASIMoDOH (RRID:SCR_018708) Copy
Benchtop genetic analyzer. Electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow.
Proper citation: Agilent: 4200 TapeStation System (RRID:SCR_018435) Copy
https://github.com/zhengkaiyu/FIMAS
Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files.
Proper citation: Fluorescent Imaging Analysis Software FIMAS (RRID:SCR_018311) Copy
https://github.com/caleblareau/mgatk
Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.
Proper citation: mgatk (RRID:SCR_021159) Copy
http://tools.thermofisher.com/content/sfs/manuals/cms_040970.pdf
Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C.
Proper citation: Thermo Fisher: Applied Biosystems: GeneAmp 9700 PCR Thermocycler System (RRID:SCR_018436) 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
Open browser to inform therapeutics development for tracking SARS-CoV-2 single nucleotide variations, lineages, and clades using virus genomes on GISAID database while filtering by location, date, gene, and mutation of interest. can Provides information on which virus mutations are present in area during specific period by processing data on mutations found in viral genetic material collected worldwide from hundreds of thousands of people with COVID-19, which are hosted in existing online database.
Proper citation: COVID CG (RRID:SCR_022266) Copy
https://github.com/wtsi-hpag/PretextMap
Software tool to convert SAM formatted read pairs into genome contact maps. Prepares alignments for visualization with PretextView.
Proper citation: PretextMap (RRID:SCR_022023) Copy
https://gitlab.com/PlantGenomicsLab/gFACs
Software package provides comprehensive framework for evaluating, filtering, and analyzing gene models from range of input applications and preparing these annotations for formal publication or downstream analysis.
Proper citation: gFACs (RRID:SCR_022017) 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
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