Showing 122 open source projects for "rna"

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  • 1
    kallisto

    kallisto

    Near-optimal RNA-Seq quantification

    kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome...
    Downloads: 2 This Week
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  • 2

    CPAT

    RNA coding potential assessment tool

    Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC...
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    Downloads: 13 This Week
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  • 3

    Subread

    High-performance read alignment, quantification and mutation discovery

    The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published...
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    Downloads: 368 This Week
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  • 4
    relax

    relax

    Molecular dynamics by NMR data analysis

    The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using...
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    Downloads: 57 This Week
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    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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  • 6

    miRge3

    Comprehensive analysis of small RNA sequencing data

    An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface...
    Downloads: 5 This Week
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  • 7
    ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.
    Downloads: 0 This Week
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  • 8
    SPiCEv2.1

    SPiCEv2.1

    Splicing Prediction in Consensus Element

    SPiCE is no longer maintained. To access the tool's predictions, please use SPiP, accessible at : https://sourceforge.net/projects/splicing-prediction-pipeline/ or https://github.com/raphaelleman/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1.5 (05/2019) + corr (01/2020): Fix bug for linux version v2.1.4 (03/2019): Proxy management (only for Windows version) v2.1.3 (07/2018): correction bug for first 3' ss import vcf...
    Downloads: 0 This Week
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  • 9
    Gemi

    Gemi

    PCR primers / probes design from multiple & degenerate sequences

    Gemi can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR...
    Downloads: 1 This Week
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  • 10
    Fusion Detection Pipeline

    Fusion Detection Pipeline

    Fusion gene detection pipeline bundled into a Singularity container.

    Fusion gene detection by RNA-seq requires prior setup of several software modules and dependencies which might be troublesome. Furthermore, fusion detection tools tend to report many false positives. Therefore, we developed a detection and filtering workflow bundled into a Singularity container for a streamlined and easy-to-use application. Arriba and FusionCatcher are utilized for fusion calling. Our filtering pipeline uses read counts generated by FeatureCounts and insert size estimation...
    Downloads: 0 This Week
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  • 11
    CStone

    CStone

    Short-read de novo assembler that identifies chimeric contigs.

    > CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/
    Downloads: 0 This Week
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  • 12

    viRome

    R code/package for virus small RNA sequence data

    Please use code here: https://github.com/mw55309/viRome_legacy
    Downloads: 0 This Week
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  • 13
    Cell Paint

    Cell Paint

    cellPAINT allows users to create living illustrations of biology.

    cellPAINT is a free-form painting app that allows users to create their own living illustrations of cellular landscapes. There are currently several prototypes available: --cellPAINT_coronavirus includes a newly-redesigned user interface, and molecular building blocks for coronavirus, blood plasma, and a simple human cell --cellPAINT_exo includes hand-painted sprites created by Julia Jimenez during an internship, and also allows input of custom sprites through Mesoscope --cellPAINT_VR is a...
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    Downloads: 21 This Week
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  • 14

    FusionCatcher

    Somatic fusion-genes finder for RNA-seq data

    FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions, CIC...
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    Downloads: 45 This Week
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  • 15

    DAMIAN

    Identification of pathogenic microorganisms in diagnostic samples

    DAMIAN provides capabilities to detect known and novel pathogens in RNA and DNA samples of various sources. It integrates all required processing steps, ranging from the quality control of sequencing reads to the generation of comprehensive reports. The method works for any host organism.
    Downloads: 1 This Week
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  • 16
    MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both...
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    Downloads: 57 This Week
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  • 17

    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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  • 18
    HyLiTE

    HyLiTE

    Hybrid Lineage Transcriptome Explorer

    HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one...
    Downloads: 0 This Week
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  • 19

    epidaurus

    tumor epigenetic database

    Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets.
    Downloads: 0 This Week
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  • 20
    TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
    Downloads: 0 This Week
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  • 21

    rRNAFinder

    Fast ribosomal RNA detector and annotator

    rRNAFinder is a small perl software package, which can be used to automatically predict and classify the ribosome RNA genes using the assembled genome/metagenome contigs as input. The software were only tested on the Linux operating system. "rRNAFinder.pl" program included in the package uses nhmmer program searching against the arc.hmm, bac.hmm, and euk.hmm databases to identify rRNA genes from the input contigs. The predicated rRNA genes include 16S, 18S, 23S, 28S, 5S, and 5.8S rRNA genes...
    Downloads: 0 This Week
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  • 22

    reditools

    RNA editing detection by NGS data

    REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data. RNA editing is a post-transcriptional phenomenon involving the insertion/deletion or substitution of specific bases in precise RNA localizations. In human, RNA editing occurs by deamination of cytosine to uridine (C-to-U) or mostly by the adenosine to inosine (A-to-I) conversion through ADAR enzymes. A-to-I substitutions may have profound functional consequences and have...
    Downloads: 0 This Week
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  • 23

    HSRA

    Hadoop spliced read aligner for RNA-seq data

    HSRA is a MapReduce-based parallel tool for mapping reads from RNA sequencing (RNA-seq) experiments. RNA-seq analyses typically begin by mapping reads to a reference genome in order to determine the location from which the reads were originated, which is a very time-consuming step. This tool allows bioinformatics researchers to efficiently distribute their mapping tasks over the nodes of a cluster by combining a fast multithreaded spliced aligner (HISAT2) with Apache Hadoop, which...
    Downloads: 0 This Week
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  • 24

    packeis

    Check for selection of RNA secondary structure

    PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons.
    Downloads: 0 This Week
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  • 25

    rMATS-ISO

    rMATS-Iso is a generalization of rMATS for complex splicing patterns.

    rMATS-Iso is a generalization of the rMATS statistical framework, to detect differential splicing modules with complex splicing patterns using replicate RNA-seq data.
    Downloads: 0 This Week
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