Showing 169 open source projects for "seq"

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  • 1

    PRADA

    PRADA : Pipeline for RNA-Sequencing Data Analysis

    Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify abnormalities...
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  • 2
    SATRAP01

    SATRAP01

    SOLiD Assembler TRAnslation Program

    SATRAP, a computer program designed to efficiently translate de novo assembled color-space sequences into base-space. The program was tested and validated using simulated and real transcriptomics data; its modularity allows easy integration into more complex pipelines, such as Oases for RNA-seq de novo assembly.
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  • 3

    MSProGene

    Integrative proteogenomics beyond six-frames and SNPs

    MSProGene constructs customized transcript databases for tandem mass spectra search. RNA-Seq data is used to generate transcripts and to resolve shared peptide protein inference in a proteogenomic network.
    Downloads: 0 This Week
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  • 4
    EBARDenovo

    EBARDenovo

    Highly-accurate de novo assembler of paired-end RNA-Seq

    A highly-accurate search-based de novo assembler of paired-end RNA-Seq for advance transcriptomic study.
    Downloads: 0 This Week
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  • 5
    A multi-purpose ultrafast peak caller for ChIP Seq data
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  • 6

    SimplyTheBlast

    Blast query sequences on a set of fasta formatted genomes

    SimplyTheBlast: a small perl tool to build genes presence/absence matrices over a set of Fasta formatted genomes. This code requires: Bio::SeqIO; Bio::Perl; Bio::Tools::Run::StandAloneBlast; Bio::Seq; Bio::Tools::Blast; Bio::DB::GenBank; Bio::DB::WebDBSeqI; and BLAST 2.2.28 (blastall and formatcmd) installed and reachable from your command line Usage: perl SimplyTheBlast-Align.pl <fasta formatted seeds file> <path to genomes folder> <Alignment length threshold in %> <Alignment...
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  • 7
    This page contains the necessary software to characterize mappability of RNA-Seq reads and create a "blacklist" of genomic positions of mismapped reads. This blacklist can be used to filter potential false positives from variant or RNA editing calls. This software is described in "BlackOPs: Increasing Confidence in Variant Detection through Mappability Filtering" by CR Cabanski et al. Please cite this article if you use our software or available blacklists in your own analysis.
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  • 8
    COV2HTML

    COV2HTML

    A visualization and analysis tool of Bacterial NGS data for Biologists

    ... mapping coverage data (DNA-seq, RNA-seq, ChIP-seq and TSS) performed in different prokaryotic organisms (bacteria, viruses...) or different experimental conditions (mutant versus wild type strains or different growth states…) facilitating studies.
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  • 9
    rseqflow

    rseqflow

    RNA-Seq analysis pipeline for QC, Expression, DifferentialExpression

    RseqFlow is an RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. It can perform pre and post mapping quality control (QC) for sequencing data, calculate expression levels for uniquely mapped reads, identify differentially expressed genes, and convert file formats for ease of visualization. A detailed description of the pipeline] is given here: https://sourceforge.net/p/rseqflow/wiki/PipelineDescription RseqFlow offers two run mode...
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  • 10
    Protospacer

    Protospacer

    Rapid gRNA design and validation for CRISPR

    ... by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website.
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  • 11

    traph

    A tool for transcript identification and quantification with RNA-Seq

    Traph is a novel tool for transcript identification and quantification with RNA-Seq data, based on minimum-cost flows. Our method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model.
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  • 12
    IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
    Downloads: 0 This Week
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  • 13

    pvaas

    Program to identify Variants Associated with Aberrant Splicing

    Alternative splicing is a precisely regulated process that involves interactions between cis- and trans-acting regulatory elements, and factors that disrupt these interactions can result in aberrant splicing. About 15-60% of human disease-causing mutations affect mRNA splicing rather than directly affecting coding sequences (López-Bigas, et al 2005, Krawczak M, et al, 1992). Deep transcriptome sequencing (RNA-seq) provides ability to interrogate both aberrant splicings and mutations...
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  • 14

    Deem

    Analyze time-course data with significance tests, clustering, modeling

    Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional...
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  • 15

    BRACIL

    ChIP-seq analysis tool

    Binding Resolution Amplifier and Cooperative Interaction Locator (BRACIL) is a blind-deconvolution model that integrates ChIP-seq coverage with motif discovery. BRACIL predicts binding site locations with high-resolution and also cooperative interactions in ChIP-seq data.
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  • 16

    MendelChecker

    QC for variant discovery from next gen sequence in pedigrees

    MendelChecker is a likelihood-based measure of Mendelian segregation of Single Nucleotide Polymorphisms (SNPs) in nuclear pedigrees. We developed this method as a quality control measure for novel variant discovery from noisy next-generation sequencing data in pedigrees, such as Restriction site-associated DNA Sequencing (RAD-seq) in non-model organisms. This method implements comparison of heterogametic vs. homogametic transmission, i.e., sex linked vs. autosomal segregation.
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  • 17
    DeSQ

    DeSQ

    Seq: Gestore di processi sequenziali con esecuzione da smartphone

    Progetto del corso di Ingegneria del software, Università degli Studi di Padova aa 2013/14 Gruppo DeSQ
    Downloads: 1 This Week
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  • 18

    GIIRA

    RNA-Seq driven gene finding incorporating ambiguous reads

    GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms.
    Downloads: 0 This Week
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  • 19
    CHANCE-HT

    CHANCE-HT

    ChIP-seq data pre-processing software

    CHANCE-HT is a ChIP-seq pre-processing software that filters samples with weak IP-strength, identifies heavily biased control experiments and under sequenced samples, detects batch effects, and normalizes large ensembles of ChIP-seq datasets. CHANCE-HT uses a parallel processing approach to normalize and filter large collections of ChIP-seq datasets in tandem.
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  • 20

    Bycom

    Bycom can do methylcytosine calling (5mC calling) from BS-seq.

    Bycom can do methylcytosine calling from BS-seq (WGBS and RRBS), and either unmapped reads (FASTQ) or mapped reads (SAM/BAM) could be permitted for the input data. Certain SNPs (C>A/G) can also be selected in the output. 1. There's no softwares or methods identify methylcytosines considering the cell heterozygosis caused by multicellular sequencing. Bycom introduced it along with the sequencing errors and unconverson rate based on the Bayesian model. 2. Several parameters in Bycom could...
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  • 21

    snpSniffer

    snpSniffer is a sample integrity checking tool for NGS data

    -- About snpSniffer -- snpSniffer is a genotype based sample integrity checking tool for next generation sequencing data. It ensures no sample mixups have occurred by checking genotype concordance of carefully curated genomic loci. It currently works on whole genome, exome and RNA-Seq data. Identifying mixups involves 3 steps 1. Generate the genotypes in a vcf format at specific genomic loci 2. Adding the genotypes generated to a flat file "database.ini" provided 3. Compare...
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  • 22
    FineSplice

    FineSplice

    Enhanced splice junction detection and estimation from RNA-Seq data

    FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi...
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  • 23

    DNase2Hotspots

    This software identifies tag-enriched regions(hotspots) from DNase-seq

    DNase2Hotspots is a software package for identifying tag-enriched genomic regions (hotspots) from the DNase-Seq genomic data. This program reads a BAM (Binary Alignment/Map) file or tab-delimited text files as input and produces a list of hotspot candidates and associated z-scores as output. Mappability profiles for the reference genome and genomic regions of repeat maskers are also required as input.
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  • 24

    AS-peak

    ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq

    Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus identification of RNA-protein binding sites from high throughput sequencing data presents unique challenges. While peak identification in CHIP-Seq data has been extensively explored, there are few bioinformatics tools tailored to peak calling on the analogous datasets for RNA-binding proteins. Here we describe ASPeak, an implementation of an algorithm that we previously applied to detect peaks in Exon Junction Complex...
    Downloads: 8 This Week
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  • 25
    This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
    Downloads: 6 This Week
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