Showing 39 open source projects for "rna-seq"

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  • 1
    ShowEQ Open Source Project
    ShowEQ or SEQ for short is a program designed to decode the EverQuest data stream and display that information on another computer running the Linux OS in real time. Our Forums are located at https://seq.sourceforge.net/forums/
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    Downloads: 203 This Week
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  • 2
    oxDNA

    oxDNA

    A code primarily aimed at DNA and RNA coarse-grained simulations

    The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.
    Downloads: 6 This Week
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  • 3
    sRNAWorkbench

    sRNAWorkbench

    The UEA sRNA Workbench

    A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data
    Downloads: 5 This Week
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  • 4
    Lexical Analyzer Generator Quex

    Lexical Analyzer Generator Quex

    Generator of lexical analyzers in C and C++. Unicode Supported.

    The goal of this project is to provide a generator for lexical analyzers of maximum computational efficiency and maximum range of applications. This includes the support for Unicode (UTF8, UTF16, ...) and a large variety of other encodings directly and via nested converters such as ICU(tm) and IConv. Sophisticated buffer handling allows to operate on plain file streams, on sockets, or manually fed buffer content. 'Ready-to-build' examples explain related concepts and facilitate practical...
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    Downloads: 21 This Week
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  • 5

    GapFiller

    A de novo local assembler for paired reads

    GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length.
    Downloads: 7 This Week
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  • 6
    faif

    faif

    C++ header only library with AI and bioinformatics algorithms

    C++ header only library, small and fast; Naive Bayesian Classifier, Decision Tree Classifier (ID3), DNA/RNA nucleotide second structure predictor, timeseries management, timeseries prediction, generic Evolutionary Algorithm, generic Hill Climbing algorithm and others.
    Downloads: 0 This Week
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  • 7
    ds-Bidens

    ds-Bidens

    Software for studying bacterial colony features

    Software for studying bacterial colony features: Optical forward-scattering systems supported by image analysis methods are increasingly being used for rapid identification of bacterial colonies. The conventional detection and identification of bacterial colonies comprises a variety of methodologies based on biochemical, serological or DNA/RNA characterization. Such methods involve laborious and time-consuming procedures in order to achieve confirmatory results. The software (ζ-Bidens...
    Downloads: 0 This Week
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  • 8

    d64srch

    search for patterns in files on d64 images

    Call this program with a d64 image name and a hex sequence, a petscii- or a screencode-string as parameters and it will spit out the names of all files that include that pattern. Can search PRG-, SEQ- , REL-, USR- and DEL-Files and also just list the names of all files of the selected type(s) on the image. Probably not very useful, but I needed something like that a while ago, so I wrote it and here it is.
    Downloads: 0 This Week
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  • 9
    Several RNA and protein structure volume calculation tools.
    Downloads: 0 This Week
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  • 10

    PingPongPro

    Find ping-pong signatures like a pro

    ... the production of more piRNAs, thus reinforcing the anti-transposon response in a feed-forward loop called the "ping-pong cycle". A key question in ping-pong cycle research is identification of piRNAs which are amplified through the cycle. PingPongPro is a command-line tool for detecting ping-pong cycle activity in piRNA-Seq data. PingPongPro was developed at the Institute of Molecular Biology gGmbH in Mainz.
    Downloads: 1 This Week
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  • 11

    BamBam

    Tools for genomic analysis

    BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball.
    Downloads: 0 This Week
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  • 12

    LivMach Framework

    A virtual organism simulation framework written in C++

    This is a C++ code to simulate life processes and responses to external stimulii in multicellular organisms by replicating the data flow in an actual organism using a straightforward approach. It can simulate both stimulus response and life processes(like respiration,excretion etc.) at the same time using multi-threading techniques. Digital DNA simulation- translation and transcription of DNA template to RNA is now supported. Users can also simulate cells and tissues using inbuilt classes.
    Downloads: 0 This Week
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  • 13
    HeatmapGenerator
    HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research. HeatmapGenerator can also be used to make heatmaps in a variety of other non-medical fields. HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30). Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization software...
    Downloads: 2 This Week
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  • 14
    olego

    olego

    OLego – short or long RNA-seq read mapping to discover exon junction

    OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast...
    Downloads: 2 This Week
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  • 15

    Virus QSP Modeling

    C++ and Python code for simulating RNA virus replication

    Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files.
    Downloads: 0 This Week
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  • 16
    GTfold
    A Scalable Multicore Code for RNA Secondary Structure Prediction
    Downloads: 0 This Week
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  • 17
    deFuse is a software package for gene fusion discovery using RNA-Seq data. deFuse .tar.gz bundles will be released periodically on the sourceforge site, see Files. Questions can be posted to the sourceforge discussion forum. The sourceforge wiki is depracated in favour of documentation included with the package. Development of deFuse is on the bitbucket site, linked below.
    Downloads: 1 This Week
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  • 18
    FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
    Downloads: 1 This Week
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  • 19

    rnasimulase

    Simulation of allele-specific RNA-seq data

    Simulation of allele-specific RNA-seq data
    Downloads: 0 This Week
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  • 20

    HPeak

    A HMM-based algorithm for defining enriched regions from ChIP-seq data

    HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN...
    Downloads: 0 This Week
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  • 21
    NeedlemanWunsch

    NeedlemanWunsch

    Fast global sequence alignment for the masses!

    MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/
    Downloads: 0 This Week
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  • 22
    rNA is an aligner for short reads produced by Next Generation Sequencers
    Downloads: 0 This Week
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  • 23

    RNAseqR

    RNA-seq expression analysis tool

    RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems. With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by Stekel, et...
    Downloads: 0 This Week
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  • 24
    SmithWaterman

    SmithWaterman

    Fast local sequence alignment for the masses!

    MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/
    Downloads: 0 This Week
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  • 25
    YaSeTo implements a modification of the widely used Sankoff-Algorithm for sequence/structure alignments of RNA sequences. It is suitable for genome-wide ncRNA gene finding, in case the ncRNA exhibits a conserved secondary structure.
    Downloads: 0 This Week
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