Showing 73 open source projects for "mp.3"

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  • 1
    In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
    Downloads: 0 This Week
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  • 2
    GenSeed-HMM

    GenSeed-HMM

    Progressive assembly tool using DNA, protein or profile HMMs as seeds.

    GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs...
    Downloads: 1 This Week
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  • 3
    TaxOnTree

    TaxOnTree

    A program for associating taxonomic information in a phylogenetic tree

    TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software...
    Downloads: 0 This Week
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  • 4

    COHCAP

    City of Hope CpG Island Analysis Pipeline

    .... 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download
    Downloads: 0 This Week
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  • 5
    The OpenGEREA is a open enrichment analysis framework for gene expression regulation data analysis.
    Downloads: 0 This Week
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  • 6

    infix2pharmml

    Converter between mathematical infix notation and PharmML math markup.

    PharmML is a markup for pharmacometrics markup language documented at http://pharmml.org/. This project provides a converter between the conventional mathematical infix notation and the math markup used by PharmML. The online version has been disabled. Please download for offline use.
    Downloads: 0 This Week
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  • 7

    bspipe

    An End-to-End Analysis Pipeline for BS-seq

    BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files...
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  • 8
    As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the...
    Downloads: 0 This Week
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  • 9

    Panacea

    PAN And Core-gEnome Analysis

    A tool to calculate the Pan-Genome of a set of annotated genomes
    Downloads: 0 This Week
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  • 10

    MOIRAI

    Simple Scientific Workflow System for CAGE Analysis

    .... MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples.
    Downloads: 4 This Week
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  • 11

    Seqping

    Gene Prediction Pipeline for Plant Genomes

    Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data
    Downloads: 1 This Week
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  • 12

    ISVASE

    identification of sequence variant associated with splicing event

    To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data....
    Downloads: 0 This Week
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  • 13

    Placnet

    Placnet project

    ... PLACNET as: Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences. PLoS Genet 2014, 10:e1004766.
    Downloads: 0 This Week
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  • 14

    REDO

    REDO - RNA Editing Detection in Organelle

    REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in...
    Downloads: 1 This Week
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  • 15

    RGAAT

    Reference based genome assembly and annotation for new genome

    This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).
    Downloads: 0 This Week
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  • 16
    AAARF, written in PERL and with numerous adjustable parameters, identifies sequence overlaps in small shotgun sequence datasets and walks them out to create long pseudomolecules representing the most abundant repeats in a genome.
    Downloads: 0 This Week
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  • 17

    bsclient

    An interactive FTP-like command-line BaseSpace download client

    bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient
    Downloads: 0 This Week
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  • 18
    PRIMUS

    PRIMUS

    Pedigree Reconstruction and Identification of a Maximum Unrelated Set

    NEW: Download new version with Pedigree Reconstruction at primus.gs.washington.edu This versions is outdated and incomplete. Please visit the new website for the complete version of PRIMUS. We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated...
    Downloads: 0 This Week
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  • 19
    SNiPlay
    SNiPlay is a web-based pipeline and database for SNP analysis and management
    Downloads: 0 This Week
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  • 20
    PhyloTrack

    PhyloTrack

    PhyloTrack, D3.js and JBrowse for phylogeny and positioning of samples

    PhyloTrack is a JavaScript--based software tool that integrates the D3.js library for data visualization with the JBrowse tool for genome browser representation. It requires a phylogenetic tree of the common Newick data format as input, as well as three meta data files for samples, clade-defining nodes and clade color definitions - all in tab delimited format. Functionality within PhyloTrack shows the informative markers at each node in the phylogenetic tree, therefore highlighting clade...
    Downloads: 0 This Week
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  • 21

    openSEQ

    NGS compute distro proloaded with pipeline analysis software

    Forked Ubuntu 14.04 minimal install with XOrg and FluxBox desktop environment for web-based pipeline construction and job submission. HOWTO: 1) Set VM network settings to a bridged adapter type. 2) Load VM to client 3) From host: $ ssh -X ubuntu@<foobar> 'firefox && butterfly.server.py --unsecure' --- passwd = 616287xx 5) or ssh into host with X forwarding, and type runme This will launch an X-session of Firefox on the client, which will then be forwarded to the host...
    Downloads: 0 This Week
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  • 22
    miRNA Temporal Analyzer (mirnaTA)

    miRNA Temporal Analyzer (mirnaTA)

    Differential expression analysis tool for miRNAs in temporal studies

    ..., and the normalized data is analyzed using linear regression model to locate any miRNAs which are differentially expressed in a linear manner. Any miRNAs with P-value<0.05 are considered statistically significant. Remaining miRNAs which did not fit in linear model are further analyzed in two different methods: (1) if the number of time points <3, CDF of the normal distribution, and (2) if the number of time points is >= 3, ANOVA is utilized. http://www.gigasciencejournal.com/content/3/1/20
    Downloads: 4 This Week
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  • 23

    PhaseTank

    genome-wide computational identification of phasiRNAs

    Phase siRNAs (phasiRNAs) are a class of small RNAs, which triggered by miRNA-targeted cleavage and followed by DCL4-mediated production of small RNAs phased in 21-nt increments. Here, we introduce PhaseTank to systematically characterize 'miRNA → mRNA → tasiRNA → target genes' regulatory casacades in plants. With one command analysis, PhaseTank is an easy-to-use software for users.
    Downloads: 2 This Week
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  • 24

    Protdraw

    Create portable, flexible domain drawings of protein sequences

    For ProtDraw to work on MacOS Yosemite, you must install a patched Pert Tk. Go to https://github.com/eserte/perl-tk and click the Download zip button. Run the unzip command, cd to the extracted directory and follow the directions in the 'INSTALL' file (using 'sudo' if necessary). ProtDraw creates flexible, easily-interpretable and portable illustrations of the domain structures of input sequences. ProtDraw is accompanied by makeProtDraw, a helper program which runs hmmer3 on a specified...
    Downloads: 0 This Week
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  • 25

    hrefinder

    Detection of homologous recombination events from SNP data

    This software detects homologous recombination events (HREs) from SNP data. Based on SNP alleles calls and locations, it breaks the genomes into locally colinear blocks, and looks for cases where SNPs do not agree with the vertical pattern of inheritance in a phylogeny. It applies a dynamic programming algorithm to model whether changes within a block are likely a result of mutations, sequencing errors, or HRE. We use information from the nearby SNPs, so that if 1-2 alleles in a series of...
    Downloads: 0 This Week
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