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https://github.com/di-0579/spatial_tri-omics

Software repository to share the raw data processing and visualization codes used in the spatial tri-omics project.

Proper citation: spatial_tri-omics (RRID:SCR_026194) 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/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://akoyabio.github.io/phenoptr/index.html

Software R package for working with inForm data. Contains functions that make it easier to read and analyze data tables and images created by Akoya Biosciences' inForm software.

Proper citation: phenoptr (RRID:SCR_026104) Copy   

•   Source: SciCrunch Registry

https://winscp.net/eng/download.php

Free file manager, SSH File Transfer Protocol, File Transfer Protocol, WebDAV, Amazon S3, and secure copy protocol client for Microsoft Windows.

Proper citation: WinSCP (RRID:SCR_026226) Copy   

•   Source: SciCrunch Registry

https://github.com/ganlab/GALA

Softawer framework for de novo chromosome-by-chromosome assembly with long reads. Long-reads gap-free chromosome-scale assembler.

Proper citation: GALA (RRID:SCR_026184) Copy   

•   Source: SciCrunch Registry

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

Software package for optimal matching in R. Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies. Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.

Proper citation: optmatch (RRID:SCR_026185) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/ENVI

Deep learnining based variational inference method to integrate scRNA-seq with spatial transcriptomics data. ENVI learns to reconstruct spatial onto for dissociated scRNA-seq data and impute unimagd genes onto spatial data.

Proper citation: ENVI (RRID:SCR_026160) Copy   

•   Source: SciCrunch Registry

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

https://github.com/oicr-gsi/ESTIMATE

Software application provides researchers with scores for tumor purity, level of stromal cells present, and infiltration level of immune cells in tumor tissues based on expression data.

Proper citation: ESTIMATE (RRID:SCR_026090) 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://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