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https://nemoanalytics.org/

Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.

Proper citation: NeMO Analytics (RRID:SCR_018164) Copy   

•   Source: SciCrunch Registry

https://github.com/WangHYLab/fcirc

Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.

Proper citation: Fcirc (RRID:SCR_018090) Copy   

•   Source: SciCrunch Registry

http://www.syglass.io

Software visualization tool for direct volume rendering with no segmentation required. Enables users to view, annotate and analyze 3D data in VR. Data visualization and annotation system that allows rendering of large, volumetric data in its true, three- or four-dimensional form.

Proper citation: syGlass (RRID:SCR_017961) Copy   

•   Source: SciCrunch Registry

http://www.prc.boun.edu.tr/appserv/prc/hingeprot/index.html

Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures.

Proper citation: HingeProt (RRID:SCR_018136) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/TCGAbiolinks/

Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy   

•   Source: SciCrunch Registry

https://www.adobe.com/lightroom

Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device.

Proper citation: Adobe Photoshop Lightroom (RRID:SCR_018012) Copy   

•   Source: SciCrunch Registry

https://isb-cgc.appspot.com/

Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform.

Proper citation: ISB Cancer Genomics Cloud (RRID:SCR_017681) Copy   

•   Source: SciCrunch Registry

https://seaborn.pydata.org/

Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib.

Proper citation: seaborn (RRID:SCR_018132) Copy   

•   Source: SciCrunch Registry

https://github.com/ctlab/GADMA

Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.

Proper citation: GADMA (RRID:SCR_017680) Copy   

•   Source: SciCrunch Registry

http://143.169.238.105/variantdb/index.php?page=variants

Web based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. Allows filtering by all annotations, under dominant, recessive or de novo inheritance models. Flexible annotation and filtering portal for next generation sequencing data.

Proper citation: VariantDB (RRID:SCR_018010) Copy   

•   Source: SciCrunch Registry

http://omnitech-usa.com/product/Fusion-Software/510

Software for analyzing mouse behavior by Omnitech Electronics Inc.

Proper citation: Fusion software (RRID:SCR_017972) Copy   

•   Source: SciCrunch Registry

https://crispy.secondarymetabolites.org

Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction.

Proper citation: CRISPy-web (RRID:SCR_017970) Copy   

•   Source: SciCrunch Registry

https://leora-software.com/products/poloplusonline

Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB.

Proper citation: PoloPlus USB Drive software (RRID:SCR_017614) Copy   

•   Source: SciCrunch Registry

https://github.com/slimsuite/pafscaff

Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly.

Proper citation: PAFScaff (RRID:SCR_017976) Copy   

•   Source: SciCrunch Registry

http://bit.do/canidmeth-github

Software tool for visualisation and quantification of DNA methylation at candidate features.

Proper citation: CandiMeth (RRID:SCR_017974) Copy   

•   Source: SciCrunch Registry

http://compbio.mit.edu/ChromHMM/

Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.

Proper citation: ChromHMM (RRID:SCR_018141) Copy   

•   Source: SciCrunch Registry

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://www2.bri.nrc.ca/ccb/pub/sietraj_main.php

Software tool for binding free energies from Amber-generated MD trajectories. Alternative to MM-PBSA software provided by AMBER distribution. Virtual alanine mutations are also possible. Solvated interaction energies are calculated using parameters that have been fitted to reproduce binding free energies of data set of 99 protein-ligand complexes.

Proper citation: sietraj (RRID:SCR_018021) 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

https://www.mbfbioscience.com/wormlab

Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays.

Proper citation: Worm Lab (RRID:SCR_017669) Copy   

•   Source: SciCrunch Registry