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https://painseq.shinyapps.io/harmonized_painseq_v1/

Harmonized cell atlases using sc/snRNA-seq data obtained from dorsal root ganglia and trigeminal ganglio mammalian datasets.

Proper citation: Harmonized DRG and TG Reference Atlas (RRID:SCR_025720) Copy   

•   Source: SciCrunch Registry

https://med.uth.edu/ibp/cam/

Microscopy facility serving Texas Medical Center. Facilitates utilization of advanced light microscopy techniques and quantitative image analysis to advance research programs of McGovern Medical School, UTHealth, and the greater Texas Medical Center. Fluorescence microscopy and image analysis core.

Proper citation: UTHealth Houston Center for Advanced Microscopy Core Facility (RRID:SCR_025962) Copy   

•   Source: SciCrunch Registry

https://www.pedsresearch.org/research/cores/biostatistics-core/overview/

Offers statistical expertise and services. Provides assistance and collaboration in study design, grant applications, protocol development, data analysis, publication preparation, and statistical education.

Proper citation: Emory University Pediatric Biostatistics Core Facility (RRID:SCR_025834) Copy   

•   Source: SciCrunch Registry

https://singlecellcore.hms.harvard.edu

Core specializes in single cell and spatial transcriptomics, and multiomics. Provides custom services, education, training and expertise in multiple high-throughput single cell technologies.

Proper citation: Harvard Medical School Single Cell Core Facility (RRID:SCR_025837) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/bwa-meth

Software tool for fast and accurate alignment of BS-Seq reads using bwa-mem and 3-letter genome.

Proper citation: BWA-METH (RRID:SCR_025851) Copy   

•   Source: SciCrunch Registry

https://qb3.berkeley.edu/facility/pmsl/

Core provides multidimensional LC-MS/MS analysis including Protein ID, Proteomics Profiling, Targeted Proteomics and Post Translational Modification analysis. Quantitative proteomic services are provided using label free quantitative proteomic (LFQ) profiling, Tandem mass tagging (TMT) or SILAC approaches. Provides support for macromolecular complexes using Nano ESI.

Proper citation: University of California at Berkeley Vincent J. Coates Proteomics/Mass Spectrometry Laboratory Core Facility (RRID:SCR_025852) Copy   

•   Source: SciCrunch Registry

https://www.php.net/

Popular general-purpose scripting language that is especially suited to web development.

Proper citation: PHP (RRID:SCR_025974) Copy   

•   Source: SciCrunch Registry

https://www.homd.org/

Provides comprehensive curated information on bacteria in human mouth and aerodigestive tract, including pharynx, nasal passages, sinuses and esophagus. eHOMD taxonomy provides provisional naming scheme for currently unnamed taxa, based on 16S rRNA sequence phylogeny, so that strain, clone and probe data from any laboratory can be directly linked to a stably named reference scheme.

Proper citation: expanded Human Oral Microbiome Database (RRID:SCR_025964) Copy   

•   Source: SciCrunch Registry

https://ntc.hms.harvard.edu/

Core specializes in analysis of nascent transcriptome using PRO-seq and TT-seq NGS methods. Provides services allowing users to submit prepared cells and receive analyzed data. Offers free consultations to help with experimental design, answer questions, and discuss data analysis.

Proper citation: Harvard Medical School Nascent Transcriptomics Core Facility (RRID:SCR_025844) Copy   

•   Source: SciCrunch Registry

https://github.com/cafferychen777/ggpicrust2

Software R package for analyzing and interpreting results of PICRUSt2 functional prediction. Offers range of features, including pathway name/description annotations, advanced differential abundance methods, and visualization of differential abundance results. Used for PICRUSt2 predicted functional profile analysis and visualization.

Proper citation: ggpicrust2 (RRID:SCR_025965) Copy   

•   Source: SciCrunch Registry

https://github.com/zhouhj1994/LinDA

Software linear models for differential abundance analysis of microbiome compositional data. Used to tackle compositional effects in differential abundance analysis. It fits linear regression models on centered log2-ratio transformed data, identifies bias term due to transformation and compositional effect, and corrects bias using mode of regression coefficients. It could fit mixed-effect models.

Proper citation: LinDA (RRID:SCR_025966) Copy   

•   Source: SciCrunch Registry

https://www.selenium.dev/documentation/webdriver/

Software remote control interface that enables introspection and control of user agents. Provides platform- and language-neutral wire protocol as way for out-of-process programs to remotely instruct behavior of web browsers.

Proper citation: Selenium WebDriver (RRID:SCR_025969) Copy   

•   Source: SciCrunch Registry

https://github.com/cran/PRROC

Software package for computing and visualizing precision-recall and receiver operating characteristic curves in R for weighted and unweighted data.

Proper citation: PRROC (RRID:SCR_026113) Copy   

•   Source: SciCrunch Registry

https://github.com/Rdatatable/data.table

Software R data.table package extends data.frame. Provides high-performance version of base R's data.frame with syntax and feature enhancements for ease of use, convenience and programming speed.

Proper citation: data.table (RRID:SCR_026117) Copy   

•   Source: SciCrunch Registry

https://geiselmed.dartmouth.edu/msp/

Core offers quantitative and qualitative proteomics services using LC-MS/MS technologies. Servies include sample preparation from harvested cell pellets, elutions post-enrichment or purification, or gel bands through data acquisition, quantification, and statistical analysis.

Proper citation: Dartmouth Geisel School of Medicine Biological Mass Spectrometry and Proteomics Shared Resource Core Facility (RRID:SCR_026076) Copy   

•   Source: SciCrunch Registry

https://www.virtualdub.org

Open-source software for video capture and video processing for Microsoft Windows. Designed to process linear video streams, including filtering and recompression. It uses AVI container format to store captured video. Video capture/processing utility for 32-bit and 64-bit Windows platforms. Used for processing AVI files, although it can read (not write) MPEG-1 and also handle sets of BMP images.

Proper citation: VirtualDub (RRID:SCR_026123) Copy   

•   Source: SciCrunch Registry

https://github.com/Incpink-Liu/DNA-storage-R_plus

Software provides direct mapping refence between expanded molecular alphabet and N-nary digits in the absence of high-performance transcoding algorithm at present. Transcoding scheme for DNA data storage based on expanded molecular alphabet.

Proper citation: R plus (RRID:SCR_026005) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/HVSeeker/tree/main

Software tool for distinguishing between bacterial and phage sequences. Consists of two separate models: one analyzing DNA sequences and the other focusing on proteins.

Proper citation: HVSeeker (RRID:SCR_026120) Copy   

•   Source: SciCrunch Registry

https://github.com/xuxif/DeepMEI

Software tool to detect mobile element insertion in human short read sequencing data.

Proper citation: DeepMEI (RRID:SCR_026119) Copy   

•   Source: SciCrunch Registry

https://bme-free.sites.uu.nl/

Database with products that can serve as alternative for basement membrane extracts (BMEs) for in vitro applications. BME-free database is publicly available and is part of 3Rs Research Tools Programme, which is managed and hosted by 3Rs Centre Utrecht.

Proper citation: Basement Membrane Extract (BME)-free Database (RRID:SCR_026058) Copy   

•   Source: SciCrunch Registry