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https://github.com/sanger-pathogens/assembly-stats

Software to get assembly statistics from FASTA and FASTQ files.

Proper citation: assembly-stats (RRID:SCR_023963) Copy   

•   Source: SciCrunch Registry

https://github.com/thegenemyers/DEXTRACTOR

Software as Bax file decoder and data compressor.

Proper citation: DEXTRACTOR (RRID:SCR_024005) Copy   

•   Source: SciCrunch Registry

https://github.com/nexml/nexml.java

Software repository contains java code for NeXML processing.

Proper citation: Java NeXML libraries and tools (RRID:SCR_024084) Copy   

•   Source: SciCrunch Registry

http://git-scm.com/

A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.

Proper citation: Git (RRID:SCR_003932) Copy   

•   Source: SciCrunch Registry

http://www.neuromatic.thinkrandom.com/

NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC

Proper citation: NeuroMatic (RRID:SCR_004186) Copy   

•   Source: SciCrunch Registry

https://github.com/mfumagalli/ngsTools

A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data.

Proper citation: ngsTools (RRID:SCR_005489) Copy   

•   Source: SciCrunch Registry

https://imjoy.io

Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.

Proper citation: ImJoy (RRID:SCR_020935) Copy   

•   Source: SciCrunch Registry

https://github.com/statOmics/tradeSeq

Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data.

Proper citation: tradeSeq (RRID:SCR_019238) Copy   

•   Source: SciCrunch Registry

http://srna-workbench.cmp.uea.ac.uk

Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.

Proper citation: UEA sRNA Workbench (RRID:SCR_020947) Copy   

•   Source: SciCrunch Registry

http://www.iqtree.org

Software tool for phylogenomic inference.

Proper citation: IQ TREE (RRID:SCR_021163) Copy   

•   Source: SciCrunch Registry

https://github.com/amkozlov/raxml-ng

Software phylogenetic tree inference tool which uses maximum likelihood optimality criterion. Used for maximum likelihood phylogenetic inference. Offers improved accuracy, flexibility, speed, scalability, and usability compared with RAxML/ExaML.

Proper citation: RAxML Next Generation (RRID:SCR_022066) Copy   

•   Source: SciCrunch Registry

http://topaz.gatech.edu/GeneMark/

Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark.

Proper citation: GeneMarkS-T (RRID:SCR_017648) Copy   

•   Source: SciCrunch Registry

https://www.mesquiteproject.org/

Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed.

Proper citation: Mesquite (RRID:SCR_017994) Copy   

•   Source: SciCrunch Registry

https://github.com/srp33/ShinyLearner

Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data.

Proper citation: ShinyLearner (RRID:SCR_017608) Copy   

•   Source: SciCrunch Registry

https://github.com/sysu-yanglab/TDimpute

Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data.

Proper citation: TDimpute (RRID:SCR_018306) Copy   

•   Source: SciCrunch Registry

https://github.com/oushujun/LTR_FINDER_parallel

Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons.

Proper citation: LTR_FINDER_parallel (RRID:SCR_018969) Copy   

•   Source: SciCrunch Registry

https://github.com/gevaertlab/BetaVAEImputation

Software tool as deep learning framework based on variational autoencoder to impute missing values in transcriptome and methylome data analysis.

Proper citation: betaVAEImputation (RRID:SCR_018730) Copy   

•   Source: SciCrunch Registry

https://github.com/BackofenLab/StoatyDive

Software tool to evaluate and classify predicted peak profiles to assess binding specificity of protein to its targets. Can be used for sequencing data such as CLIP-seq or ChIP-Seq, or any other type of peak profile data.

Proper citation: StoatyDive (RRID:SCR_018796) Copy   

•   Source: SciCrunch Registry

https://milaboratory.com/software/mixcr/

Software tool to processes big immunome data from raw sequences to quantitated clonotypes by MiLaboratory LLC. Universal software for analysis of T- and B-cell receptor repertoire high throughput sequencing data. Software for comprehensive adaptive immunity profiling.

Proper citation: MiXCR (RRID:SCR_018725) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/StatClonotype/

Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.

Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy   

•   Source: SciCrunch Registry