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https://github.com/AstraZeneca-NGS/VarDictJava

Software tool as variant caller for both single and paired sample variant calling from BAM files. Implements amplicon bias aware variant calling from targeted sequencing experiments, rescue of long indels by realigning bwa soft clipped reads.Novel and versatile variant caller for next generation sequencing in cancer research.

Proper citation: VarDict (RRID:SCR_023658) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/panelcn.mops.html

Software R package as CNV detection tool for targeted NGS panel data. Extension of cn.mops package. Used for detecting copy number variations in targeted next generation sequencing panel data. Suitable to use for clinical geneticists for routine clinical diagnostics.

Proper citation: panelcn.mops (RRID:SCR_023657) Copy   

•   Source: SciCrunch Registry
  

https://app.grammarly.com/

Software to correct spelling and grammar.

Proper citation: Grammarly (RRID:SCR_023778) Copy   

•   Source: SciCrunch Registry
  

https://chat.openai.com/

Artificial Iinteligence chatbot that uses natural language processing to create humanlike conversational dialogue. Notable for enabling users to refine and steer conversation towards desired length, format, style, level of detail, and language used. Sibling model to InstructGPT, which is trained to follow instruction in prompt and provide detailed response.

Proper citation: ChatGPT (RRID:SCR_023775) Copy   

•   Source: SciCrunch Registry
  

http://microscopy.anu.edu.au/

Centre for Advanced Microscopy provides open access, state-of-the art microscopy and microanalysis equipment and expertise to national and international researchers, students and industry partners in the materials and life sciences. Offers services to support experimental design, data acquisition and analysis, train users in the use of instruments and help with sample preparation, provide research collaboration.

Proper citation: ANU Centre for Advanced Microscopy Core Facility (RRID:SCR_000213) Copy   

•   Source: SciCrunch Registry
  

https://www.certara.com/software/phoenix-pkpd/

Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool.

Proper citation: WinNonlin (RRID:SCR_024504) Copy   

•   Source: SciCrunch Registry
  

https://github.com/singleron-RD/CeleScope

Software tool as collection of bioinfomatics analysis pipelines to process single cell sequencing data generated with Singleron products. Single cell analysis pipelines developed by Singleron Biotechnologies.

Proper citation: CeleScope (RRID:SCR_023553) Copy   

•   Source: SciCrunch Registry
  

http://virusdetect.feilab.net/cgi-bin/virusdetect/index.cgi

Software package to efficiently and exhaustively analyze large scale sRNA datasets for virus identification. Automated pipeline for virus discovery using deep sequencing of small RNAs.

Proper citation: VirusDetect (RRID:SCR_023669) Copy   

•   Source: SciCrunch Registry
  

https://github.com/churchmanlab/genewalk

Software for individual genes functions determination that are relevant in particular biological context and experimental condition. Quantifies similarity between vector representations of gene and annotated GO terms through representation learning with random walks on condition specific gene regulatory network. Similarity significance is determined through comparison with node similarities from randomized networks.

Proper citation: GeneWalk (RRID:SCR_023787) Copy   

•   Source: SciCrunch Registry
  

https://www.pkdcure.org/

Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.

Proper citation: PKD Foundation (RRID:SCR_000209) Copy   

•   Source: SciCrunch Registry
  

http://www.dbemt.bioinfo-minzhao.org/

Database to establish comprehnsive gene resource for epithelial-mesenchymal transition.

Proper citation: dbEMT 2 (RRID:SCR_024692) Copy   

•   Source: SciCrunch Registry
  

https://github.com/biod/sambamba

Software tool to filter SAM file for soft and hard clipped alignments

Proper citation: samclip (RRID:SCR_024330) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ekg/seqwish

Software tool for alignment to variation graph inducer.

Proper citation: seqwish (RRID:SCR_024332) Copy   

•   Source: SciCrunch Registry
  

https://github.com/rvaser/rampler

Standalone software for sampling genomic sequences.Supports two modes, random subsampling of sequencing data to desired depth and file splitting to desired size in bytes.

Proper citation: rampler (RRID:SCR_024207) Copy   

•   Source: SciCrunch Registry
  

https://github.com/cbrnr/sigviewer

Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections.

Proper citation: sigviewer (RRID:SCR_024340) Copy   

•   Source: SciCrunch Registry
  

http://sitplus.crea-si.com/index/index.html

Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities.

Proper citation: sitplus (RRID:SCR_024344) Copy   

•   Source: SciCrunch Registry
  

http://carbonyldb.missouri.edu/CarbonylDB/index.php/

Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools.

Proper citation: CarbonylDB (RRID:SCR_023924) Copy   

•   Source: SciCrunch Registry
  

https://www.transnetyx.com/colony?gad=1&gclid=CjwKCAjw8symBhAqEiwAaTA__GhOxQovqufxibmOSyRqtSo__-EMrnF9OGpdOAvAPgUOTE47h8TONBoCyMMQAvD_BwE

Software for mouse colony management. Streamlined software for simplified colony management.

Proper citation: Transnetyx Colony Management (RRID:SCR_023922) Copy   

•   Source: SciCrunch Registry
  

https://github.com/wkusmirek/mONiTor

Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process.

Proper citation: mONiTor (RRID:SCR_023921) Copy   

•   Source: SciCrunch Registry
  

http://web.mit.edu/spectroscopy/facilities/lbrc.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale.

Proper citation: Laser Biomedical Research Center (RRID:SCR_000106) Copy   

•   Source: SciCrunch Registry