Tools   Select Another Resource Report Type

https://bioconductor.org/packages/release/bioc/html/DropletUtils.html

Software R package provides number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading from count matrices or molecule information files, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.

Proper citation: DropletUtils (RRID:SCR_026136) Copy   

•   Source: SciCrunch Registry

http://ibs.biocuckoo.org/online.php

Software package called illustrator of biological sequences. Can be used for representing organization of either protein or nucleotide sequences. Multiple options are provided, and biological sequences can be manipulated, recolored or rescaled in user-defined mode. Final representational artwork can be directly exported into publication-quality figure. Used as illustrator for presentation and visualization of biological sequences. Standalone package was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available

Proper citation: Illustrator for Biological Sequences (RRID:SCR_026149) Copy   

•   Source: SciCrunch Registry

https://github.com/maia-sh/aactr

Software R client for the Aggregate Content of ClinicalTrials.gov (AACT) database API.

Proper citation: aactr (RRID:SCR_026245) Copy   

•   Source: SciCrunch Registry

https://github.com/vgl-hub/gfastats

Standalone tool to compute assembly summary statistics and manipulate assembly sequences in FASTA, FASTQ or GFA [.gz] format. Gfastats stores assembly sequences internally in a GFA-like format. This feature allows gfastats to seamlessly convert FAST* to and from GFA [.gz] files. Gfastats can also build an assembly graph that can in turn be used to manipulate the underlying sequences following instructions provided by the user, while simultaneously generating key metrics for the new sequences.

Proper citation: gfastats (RRID:SCR_026368) Copy   

•   Source: SciCrunch Registry

https://github.com/ncbi/fcs-gx

Software Foreign Contamination Screening - GX source code. Part of NCBI’s Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes.

Proper citation: FCS-GX (RRID:SCR_026367) Copy   

•   Source: SciCrunch Registry

https://github.com/openMetadataInitiative/openMINDS_chemicals

Software repository hosts one of the metadata models of the openMINDS metadata framework. It defines modular metadata schemas for describing chemical substances and mixtures.

Proper citation: openMINDS chemicals metadata model (RRID:SCR_026248) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/BayesSpace.html

Software R package for clustering and enhancing resolution of spatial gene expression experiments. Clusters low-dimensional representation of gene expression matrix, incorporating spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Proper citation: BayesSpace (RRID:SCR_026309) Copy   

•   Source: SciCrunch Registry

http://qualimap.conesalab.org/

Software platform-independent application written in Java and R that provides both Graphical User Inteface and command-line interface to facilitate quality control of alignment sequencing data and its derivatives like feature counts. Used for advanced multi-sample quality control for high-throughput sequencing data.

Proper citation: Qualimap 2 (RRID:SCR_026258) Copy   

•   Source: SciCrunch Registry

https://github.com/mwess/greedyfhist

Algorithm for registration of stained fresh frozen serial images. Used for registration of stained histology images.

Proper citation: GreedyFHist (RRID:SCR_026477) Copy   

•   Source: SciCrunch Registry

https://github.com/wilkelab/ggtext/

Software R package that enhances text rendering in ggplot2 by allowing the use of Markdown, HTML, and rich text formatting for annotations, labels, and titles in plots.

Proper citation: ggtext (RRID:SCR_026470) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ecodist

Software R package as dissimilarity-based functions for ecological analysis. Used for analyzing ecological data.

Proper citation: ecodist (RRID:SCR_026509) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/chopper

Software tool that combines the utility of NanoFilt and NanoLyse, for filtering sequencing reads based on quality, length, and contaminating sequences, delivers 7-fold speed up compared to the Python implementation, making use of the Rust-Bio library and Rust bindings to minimap2.

Proper citation: chopper (RRID:SCR_026486) Copy   

•   Source: SciCrunch Registry

https://autodocksuite.scripps.edu/adt/

Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.

Proper citation: AutoDockTools (RRID:SCR_026401) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html

Software R package for Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data assembled using data from public repositories.

Proper citation: hgu133plus2 (RRID:SCR_026448) Copy   

•   Source: SciCrunch Registry

https://github.com/spreka/biomagdsb

Software tool as parameter-free deep learning framework for nucleus segmentation using image style transfer. Cell segmentation tool.

Proper citation: NucleAIzer (RRID:SCR_026500) Copy   

•   Source: SciCrunch Registry

https://github.com/NC4Lab/NC4gate

Code for testing and operating NC4gate modules of modular gate system for autonomous control of rodent behavior. Fully customizable gate system that can be used in behavioral experiments involving rodent mazes (T-maze, Y-maze, radial arm, etc.).

Proper citation: NC4gate (RRID:SCR_026445) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=timeROC

Software R package for estimation of time-dependent ROC curve and area under time dependent ROC curve in the presence of censored data, with or without competing risks. Confidence intervals of AUCs and tests for comparing AUCs of two rival markers measured on the same subjects can be computed, using the iid-representation of the AUC estimator.

Proper citation: timeROC (RRID:SCR_026444) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=hdf5r

Software R package as data model, library and file format for storing and managing large amounts of data.

Proper citation: hdf5r (RRID:SCR_026447) Copy   

•   Source: SciCrunch Registry

https://github.com/agshumate/Liftoff

Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations.

Proper citation: Liftoff (RRID:SCR_026535) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/gettext/

Software tools that provide framework to help other GNU packages produce multi-lingual messages.

Proper citation: gettext (RRID:SCR_026490) Copy   

•   Source: SciCrunch Registry