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https://github.com/AndreMacedo88/VEnCode

Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases.

Proper citation: VEnCode (RRID:SCR_018024) Copy   

•   Source: SciCrunch Registry

https://github.com/cramerlab/warp

Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising.

Proper citation: Warp (RRID:SCR_018071) Copy   

•   Source: SciCrunch Registry

http://raptorx.uchicago.edu/

Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model.

Proper citation: RaptorX (RRID:SCR_018118) Copy   

•   Source: SciCrunch Registry

https://clipseq.usegalaxy.eu/

Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP.

Proper citation: CLIP-Explorer (RRID:SCR_018128) Copy   

•   Source: SciCrunch Registry

https://github.com/lmcinnes/umap

Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data.

Proper citation: Umap (RRID:SCR_018217) Copy   

•   Source: SciCrunch Registry

https://github.com/BUStools/bustools/

Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks.

Proper citation: Bustools (RRID:SCR_018210) Copy   

•   Source: SciCrunch Registry

https://huygens.science.uva.nl/PlotTwist/

Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics.

Proper citation: PlotTwist (RRID:SCR_018331) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/CRISPRcasIdentifier

Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes.

Proper citation: CRISPRcasIdentifier (RRID:SCR_018296) Copy   

•   Source: SciCrunch Registry

https://www.sympy.org/en/index.html

Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible.

Proper citation: SymPy (RRID:SCR_018417) Copy   

•   Source: SciCrunch Registry

https://github.com/smortezah/smashpp

Software tool to find and visualize rearrangements in DNA sequences.

Proper citation: smashpp (RRID:SCR_018307) Copy   

•   Source: SciCrunch Registry

http://sumosp.biocuckoo.org.

Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup.

Proper citation: GPS-SUMO (RRID:SCR_018261) Copy   

•   Source: SciCrunch Registry

https://github.com/bcgsc/NanoSim

Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software.

Proper citation: NanoSim (RRID:SCR_018243) Copy   

•   Source: SciCrunch Registry

https://github.com/yanzhanglab/Graph2GO

Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology.

Proper citation: Graph2GO (RRID:SCR_018726) Copy   

•   Source: SciCrunch Registry

https://www.biosimulations.org/

Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell.

Proper citation: BioSimulations (RRID:SCR_018733) Copy   

•   Source: SciCrunch Registry

https://github.com/xiaeryu/SpoTyping-v2.0

Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads.

Proper citation: SpoTyping (RRID:SCR_018466) Copy   

•   Source: SciCrunch Registry

https://rvista.dcode.org/

Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.

Proper citation: rVista (RRID:SCR_018707) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry

http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx

Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers.

Proper citation: DAMBE (RRID:SCR_018528) Copy   

•   Source: SciCrunch Registry

https://www.bpforms.org

Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.

Proper citation: BpForms (RRID:SCR_018653) Copy   

•   Source: SciCrunch Registry