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on page 1 showing 5 out of 5 results

    BEAST2

Cite this (BEAST2, RRID:SCR_017307)

URL: https://www.beast2.org/

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

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    CHiCAGO

Cite this (CHiCAGO, RRID:SCR_014941)

URL: http://regulatorygenomicsgroup.org/chicago

Resource Type: Resource, software resource, software application, data analysis software, data processing software, software toolkit

Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values.

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Cite this (InterProScan, RRID:SCR_005829)

URL: http://www.ebi.ac.uk/Tools/pfa/iprscan/

Resource Type: Resource, data analysis service, data analysis software, data processing software, data access protocol, production service resource, analysis service resource, software application, web service, service resource, software resource

Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.

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    scran

Cite this (scran, RRID:SCR_016944)

URL: https://bioconductor.org/packages/release/bioc/html/scran.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.

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    Velvet

Cite this (Velvet, RRID:SCR_010755)

URL: http://www.molecularevolution.org/software/genomics/velvet

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux.

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