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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders Resource Report Resource Website |
University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders (RRID:SCR_000014) | Pitt CCNMD, Conte Center | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. Integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University. | schizophrenia, gaba |
has parent organization: University of Pittsburgh; Pennsylvania; USA is parent organization of: University of Pittsburgh Brain Tissue Donation Program |
NIMH 5P50MH103204-03 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144496 | SCR_000014 | SciCrunch Registry | Conte Center for the Neuroscience of Mental Disorders | 2026-09-26 02:18:06 | 0 | ||||||
|
python-bx Resource Report Resource Website 10+ mentions |
python-bx (RRID:SCR_024202) | software library, software resource, software toolkit | Software Python library and associated set of scripts for rapid implementation of genome scale analyses. | rapid implementation of genome scale analyses, | is listed by: Debian | OMICS_18239 | https://sources.debian.org/src/python3-bx/ | SCR_024202 | SciCrunch Registry | 2026-09-26 02:18:02 | 49 | |||||||||
|
saint Resource Report Resource Website 100+ mentions |
saint (RRID:SCR_024324) | SAINT | software resource, software toolkit | Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments. | assigning confidence scores, protein-protein interactions, quantitative proteomics data, AP-MS experiments, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_16243 | https://sources.debian.org/src/saint/ | SCR_024324 | SciCrunch Registry | Significance Analysis of INTeractome | 2026-09-26 02:18:05 | 231 | ||||||
|
readucks Resource Report Resource Website |
readucks (RRID:SCR_024315) | software resource, software toolkit | Software package as Nanopore read de-multiplexer. | Nanopore, read de-multiplexer, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/readucks/ | SCR_024315 | SciCrunch Registry | 2026-09-26 02:18:05 | 0 | |||||||||
|
Machine Learning Made Easy Resource Report Resource Website 1+ mentions |
Machine Learning Made Easy (RRID:SCR_024439) | MLme | software resource, software toolkit | Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis. | Machine Learning Driven Data Analysis, | Federal Ministry of Education and Research of Germany ; NIDDK R01 DK127673; Swiss National Science Foundation ; Wings for Life Spinal Cord Research Foundation |
PMID:37461685 | Free, Available for download, Freely available | SCR_024439 | SciCrunch Registry | 2026-09-26 02:18:05 | 1 | ||||||||
|
stringi Resource Report Resource Website |
stringi (RRID:SCR_024319) | software resource, software toolkit | Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing. | pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-stringi/ | SCR_024319 | SciCrunch Registry | 2026-09-26 02:18:05 | 0 | |||||||||
|
VARNA Resource Report Resource Website 10+ mentions |
VARNA (RRID:SCR_024373) | software resource, software toolkit | Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments. | Java, secondary structure of RNA drawing, secondary structure of RNA visualization, secondary structure of RNA annotation, | is listed by: Debian | PMID:19398448 | Free, Available for download, Freely available, | OMICS_04455 | https://sources.debian.org/src/varna/ | SCR_024373 | SciCrunch Registry | , Visualization Applet for RNA, varna | 2026-09-26 02:18:05 | 12 | ||||||
|
preprocesscore Resource Report Resource Website 50+ mentions |
preprocesscore (RRID:SCR_024254) | software resource, software toolkit | Software library of core preprocessing routines. | core preprocessing routines, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-preprocesscore/ | SCR_024254 | SciCrunch Registry | 2026-09-26 02:18:03 | 63 | |||||||||
|
qusage Resource Report Resource Website 1+ mentions |
qusage (RRID:SCR_024255) | software resource, software toolkit | Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies. | test for gene expression studies, | is listed by: Debian | PMID:23921631 | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-qusage/ | SCR_024255 | SciCrunch Registry | Quantitative Set Analysis for Gene Expression | 2026-09-26 02:18:03 | 3 | |||||||
|
rsamtools Resource Report Resource Website 50+ mentions |
rsamtools (RRID:SCR_024257) | software resource, software toolkit | Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files. | tabix interface, samtools interface, bcftools interface, Sequence Alignment Map manipulation, SAM manipulation, FASTA manipulation, binary variant call manipulation, compressed indexed tab delimited files manipulation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-rsamtools/ | SCR_024257 | SciCrunch Registry | 2026-09-26 02:18:03 | 61 | |||||||||
|
savr Resource Report Resource Website |
savr (RRID:SCR_024258) | software resource, software toolkit | Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots. | parse Illumina Sequence Analysis Viewer files, access data, generate QC plots, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_15992 | https://sources.debian.org/src/r-bioc-savr/ | SCR_024258 | SciCrunch Registry | 2026-09-26 02:18:03 | 0 | ||||||||
|
nanostringqcpro Resource Report Resource Website 1+ mentions |
nanostringqcpro (RRID:SCR_024250) | software resource, software toolkit | Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output. | assess quality of NanoString mRNA gene expression data, identify outlier probes and outlier samples, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-nanostringqcpro/ | SCR_024250 | SciCrunch Registry | 2026-09-26 02:18:03 | 7 | |||||||||
|
variation graph Resource Report Resource Website |
variation graph (RRID:SCR_024369) | vg | software resource, software toolkit | Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes. | read mapping, representing genetic variation in reference, encoding of sequences, genome | is listed by: Debian | PMID:30125266 | Free, Available for download, Freely available, | https://sources.debian.org/src/vg/ | SCR_024369 | SciCrunch Registry | variationgraph | 2026-09-26 02:18:05 | 0 | ||||||
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pwmenrich Resource Report Resource Website 1+ mentions |
pwmenrich (RRID:SCR_024249) | software resource, software toolkit | Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation. | DNA motif scanning and enrichment analysis, Biostrings, PWM enrichment analysis, PWM scanning and visualisation, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-pwmenrich/ | SCR_024249 | SciCrunch Registry | 2026-09-26 02:18:03 | 3 | |||||||||
|
xvector Resource Report Resource Website |
xvector (RRID:SCR_024263) | software resource, software toolkit | Software R package provides memory efficient S4 classes for storing sequences externally. | provides memory efficient S4 classes, storing sequences externally, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-bioc-xvector/ | SCR_024263 | SciCrunch Registry | 2026-09-26 02:18:03 | 0 | |||||||||
|
Trinculo Resource Report Resource Website |
Trinculo (RRID:SCR_024384) | software resource, software toolkit | Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping. | carrying out genetic association for multi-catagory phenotypes, incorporating covariates, conditional analysis, mapping | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/trinculo/ | SCR_024384 | SciCrunch Registry | trinculo | 2026-09-26 02:18:05 | 0 | ||||||||
|
BoolNet Resource Report Resource Website 1+ mentions |
BoolNet (RRID:SCR_024264) | software resource, software toolkit | Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks. | reconstruct, generate, simulate, synchronous, asynchronous, probabilistic, temporal, Boolean networks, | is listed by: Debian | PMID:20378558 | Free, Available for download, Freely available, | OMICS_06963 | https://sources.debian.org/src/r-cran-boolnet/ | SCR_024264 | SciCrunch Registry | BoolNet: Construction, Simulation and Analysis of Boolean Networks, r-cran-boolnet | 2026-09-26 02:18:03 | 2 | ||||||
|
cmprsk Resource Report Resource Website 1+ mentions |
cmprsk (RRID:SCR_024265) | software resource, software toolkit | Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks. | estimation, testing, regression modeling, subdistribution functions in competing risks, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-cmprsk/ | SCR_024265 | SciCrunch Registry | cmprsk: Subdistribution Analysis of Competing Risks, r-cran-cmprsk | 2026-09-26 02:18:03 | 3 | ||||||||
|
bio3d Resource Report Resource Website 100+ mentions |
bio3d (RRID:SCR_024266) | software resource, software toolkit | Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data. | comparative analysis of protein structures, process protein structure, organize and explore protein structure, sequence and dynamics data, | is listed by: Debian | PMID:16940322 | Free, Available for download, Freely available, | OMICS_12577 | https://sources.debian.org/src/r-cran-bio3d/ | SCR_024266 | SciCrunch Registry | r-cran-bio3d, bio3d: Biological Structure Analysis | 2026-09-26 02:18:03 | 341 | ||||||
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DoseFinding Resource Report Resource Website 1+ mentions |
DoseFinding (RRID:SCR_024268) | software resource, software toolkit | Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology. | dose finding experiments design and analysis functions, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-dosefinding/ | SCR_024268 | SciCrunch Registry | DoseFinding: Planning and Analyzing Dose Finding Experiments, r-cran-dosefinding | 2026-09-26 02:18:04 | 1 |
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