Search Results for "seq" - Page 3
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Showing 268 open source projects for "seq"
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“OMXmulti” is a user library for Ircam's OpenMusic programming environment. The library contains a single object that can be used as a replacement for both OpenMusic's regular “chord-seq” and “multi-seq” score editors. The last version (1.43) is available for OpenMusic 6.9 to 7.0. We are looking for developers, please contact at davintxi@gmail.com if you are interested. Thanks. :-) We accept donations via transfer to keep this project working. Contact at davintxi@gmail.com Thanks! :-)
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miARma-Seq
a A suite designed to study mRNAs, miRNAs and circRNAs
miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow. As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together well-established... -
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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... -
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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. -
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hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
hppRNA package is dedicated to the RNA-Seq analysis for a large number of samples simultaneously from the very beginning to the very end, which is formulated in Snakemake pipeline management system. It starts from fastq files and will produce gene/isoform expression matrix, differentially-expressed-genes, sample clusters as well as detection of SNP and fusion genes by combination of the state-of-the-art software. The first version handles protein-coding genes, lncRNAs and circRNAs and includes... -
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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. PWMScan takes as... -
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rattransc
RatTransc: a rat long noncoding RNA database
Welcome to RatTransc Introduction Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads in combination with RefSeq and UniGene annotated RNAs, we identify 39,154 lincRNA... -
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BNNPT
A powerful method for nonlinear dependence of two continuous variables
... estimator of Y based on the bagging neighborhood structure. The square error was calculated to measure how good Y is predicted by X. Finally, permutation test was applied to detect the significance of the observed square error. To evaluate the strength of BNNPT compared to seven other methods, we performed extensive simulations to explore the relationship between methods and compared the false positive rates and statistical power using both simulated and real RNA-seq datasets. -
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bspipe
An End-to-End Analysis Pipeline for BS-seq
... for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq. -
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DGEEE
Differential gene expression from exon expression RNA-Seq
Differential gene expression analysis in correlated RNA-Seq data -
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dmrs
Comprehensive evaluation of differential methylation analysis methods
... methylation analysis methods to lay out potential strengths and limitations of each method. We find that there are large differences among methods and there is no single method always ranks first in all benchmarking. Moreover, smoothing seems help to improve the performance much and small number of replicates brings more difficulties in computational analysis of BS-seq data rather than low sequencing depth. -
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We introduce a nonparametric Bayesian clustering method for inhomogeneous Poisson processes to detect heterogeneous binding patterns of multiple proteins including transcription factors. The estimated protein clusters form regulatory modules in different chromatin states, which help explain how proteins work together in regulating gene expression. We applied this approach on ChIP-seq data for mouse neural stem cells containing 21 proteins and observed different groups or modules of proteins...
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CSBB-v2.1 [CSBB-v3.0 is now available]
Computational Suite For Bioinformaticians and Biologists
... and Windows platforms. Currently CSBB provides 17 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc. -
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CSBB-v3.0
CSBB - Computational Suite for Bioinformaticians and Biologists
CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux,... -
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Genobuntu
Genobuntu Package for Next Generation Sequencing
Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one’s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build ... -
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cash-program
Comprehensive alternative splicing hunting
CASH (Comprehensive alternative splicing hunting) is visualized and user-friendly software that aims to self-construct AS (alternative splicing) sites and detect differential AS events between samples of RNA-Seq data. CASH consists of two major stages: SpliceCons (Splice site Construction) and SpliceDiff (differential AS detection). By comprehensively reconstructing AS sites from RNA-seq data, SpliceCons increases the recognition of AS events considerably and subsequently, SpliceDiff uses two... -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration... -
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BisSNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other... -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
This project contains Python scripts usable for a dual transcript-discovery approach that improves the delimitation of gene features from RNA-seq data in the chicken model. Documentation: http://bio.biologists.org/content/biolopen/suppl/2018/01/17/bio.028498.DC1/BIO028498supp.pdf Citation: Orgeur M., Martens M., Börno S. T., Timmermann B., Duprez D. and Stricker S. (2018). A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken... -
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