Search Results for "miarma-seq" - Page 5
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Showing 225 open source projects for "miarma-seq"
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QAmiRSeq
A strand aware pipeline for accurate quantification of miRNAs/isomiRs
...QAmiRSeq is a powerful and flexible open source tool for accurate quantification of known miRNAs/isomiRs from both small and large number of samples. The software package, and the test run results for miRNA-seq dataset GSE64977(human), GSE65920(mouse) and GSE60900(rat) can be downloaded directly from https://sourceforge.net/projects/qamirseq/files/, and are also available online https://baohongz.github.io/QAmiRSeq/ -
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SpliceSim is a collection of Python scripts designed for realistic simulation of RNA-seq reads for in silico differential AS studies. For software support and information on their distribution licenses, please proceed to: https://github.com/mingjiewong/SpliceSim
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BRACIL-IA
Inference of Genome Accessibility in Bacteria from ChIP-seq data.
...Transcription factors need physical access to DNA it can potentially bind. However, prior to this work it was impossible to measure and assess DNA accessibility in bacteria. This code uses ChIP-seq from multiple experiments to infer the hidden variable for genome accessibility. This is performed by a linear mixed effect model that considers two parameters: DNA affinity and DNA accessibility. The fundaments for this code and its biological relevance is described in the following reference: Gomes ALC, Wang HH (2016) The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. ... -
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iSRAP is an integrated Small RNA-seq Analysis Pipeline that aims to assess sequence quality and examine differentially expressed microRNA and other small non-coding RNAs.
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Pathoscope
Predicts strains of genomes in Nextgen seq alignment file (sam/bl8)
This page is here for archival purpose. Please visit github for the latest version of the software: https://github.com/pathoscope PathoScope takes next-generation sequencing reads from a mixture sample and predicts which genomes are present. We use a Bayesian framework combined with an initial reference-based alignment to assign reads to the correct genome of origin. Pathoscope 2.0: Wiki: http://sourceforge.net/p/pathoscope/wiki/Home/... -
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Phylobuntu is a software package that contains 37 software tools related to phylogenetic profile trees. Phylobuntu aims to provide a complete workstation for phylogenetic analysis
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Strandseq-InvertR
predicts inversions in Strand-seq data
Invert.R is a custom, R-based bioinformatic package that localizes and genotypes putative inversions in single cells. The program systematically assesses strand orientation of Strand-seq libraries using a read-based sliding window strategy to calculate Watson-Crick ratios. It assigns locale strand states based on these ratios and predicts inversions based on regional changes in strand state. The source code of this package is freely available. -
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PingPongPro
Find ping-pong signatures like a pro
...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. -
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in "Files" section) ############# GitHub : https://github.com/jbrayet/ncpro-seq... -
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
...Recently, numerous studies have employed these two approaches together, but downstream data analyses were performed separately, which always generated incongruent or conflict signals on both taxonomic and functional classifications. Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene Flanking Region Sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. We demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. -
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Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.
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EPIG-Seq
Extracting Patterns and Identifying co-expressed Genes from RNA-Seq
An algorithm and software to identify gene expression patterns from RNA-Seq count data. Once the patterns are identified, co-expressed genes are clustered to the patterns. -
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mRIN
Assessing mRNA integrity directly from RNA-Seq data
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Deep Sense
Web-interface Application for DE pipelines in RNA-seq studies
Deep Sense is a collection of open-source R web-interface applications designed for fast, simple and convenient comparisons and performance analyses of gene-level DE results from RNA-seq studies with 7 R/ Bioconductor DE pipelines: edgeR, DESeq, DESeq2, NOISeq, baySeq, EBSeq and SAMseq where users are allowed to adjust the appropriate settings for the threshold FDR values and the type of normalization procedures for their experimental needs. For software support and information on their distribution licenses, please proceed to: https://github.com/mingjiewong/Deep-Sense -
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allim
Allelic imbalance meter (Allim), a new tool for measuring allele speci
Allim, Allelic imbalance meter, offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species. Allim estimates allelic imbalance in F1 hybrids. Since mapping bias is the largest problem for reliable estimates of allele specific gene expression using RNA-seq, Allim combines two different measures to account for mapping biases. First, Allim generates a polymorphism aware reference genome that accounts for the sequence variation between the alleles of both parents (or parental lines). Second, Allim includes a sequence specific simulation tool to estimate the remaining mapping bias. This estimated mapping bias is then incorporated in the statistical tests for allelic imbalance -
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Jafaran
Fast and more random implementations of java.util.Random.
Jafaran (Java Fast Random) provides fast, and for some more random, implementations of java.util.Random, with additional nextXXX() methods, and methods to retrieve and restore state. The names of implementations contain "Conc" (for concurrent) if they are thread-safe and non-blocking, or "Seq" (for sequential) if they are not thread-safe. Also provides an implementation of Ziggurat algorithm (based on J. A. Doornik paper, 2005), used by nextGaussian() methods of the provided implementations. Requires Java 5 or later. Also available on github since 2015/12/13: https://github.com/jeffhain/jafaran Principal classes: - Implementations using Mersenne-Twister algorithm (good pseudo-randomness): MTSyncRNG MTSeqRNG - Implementations using Marsaglia Xor-Shift (fast): MXSIntSeqRNG (32 bits) MXSLongSeqRNG (64 bits) (nextLong() faster, larger period) - Ziggurat: Random-based implementation of Ziggurat algorithm. -
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SOAPfuse
a tool for identifying fusion transcripts from paired-end RNA-Seq data
SOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data. By comparing with previously released tools, SOAPfuse has a good performance. It is developed in perl, and only be used on linux OS. It requires about 8G memory to run whole analysis. So far, it is developed only for analysis on human being RNA-Seq data. SOAPfuse has been published as Method article in Genome Biology, please check http://genomebiology.com/2013/14/2/R12 The official website (*outdated) of SOAPfuse is http://soap.genomics.org.cn/soapfuse.html The wiki home of SOAPfuse is https://sourceforge.net/p/soapfuse/wiki/Home The GitHub repository of SOAPfuse Perl module is https://github.com/Nobel-Justin/SOAPfuse_PM -
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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. -
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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. -
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3C-analyzer
The detection of chromatin interactions
3C-analyzer is a computational method used for the detection of significant chromatin interactions from 3C-seq. -
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came
Identification of chromatin accessibility from NOMe-seq
...Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. However, there is no computational method for analyzing NOMe-seq data. Results: In this article, we present CAME, a seed-extension based approach that identifies chromatin accessibility from NOMe-seq. The efficiency and effectiveness of CAME were demonstrated through comparisons with other existing techniques on both simulated and real data, and the results show that our method not only can precisely identify chromatin accessibility but also outperforms other methods. -
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EDDA
Experiment Design for Differential Abundance Analysis
EDDA is a tool for systematic assessment of the impact of experimental design and the statistical test used on the ability to detect differential abundance. EDDA can aid in the design of a range of common experiments such as RNA-seq, ChIP-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. More details of EDDA can be found at Luo, Huaien et al. “The Importance of Study Design for Detecting Differentially Abundant Features in High-Throughput Experiments.” ... -
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SAT-Assembler
Scalable and accurate targeted gene assembly for large-scale NGS data
SAT-Assembler is a scalable and accurate gene assembly tool for large-scale RNA-Seq and metagenomic data. It recovers genes from gene families of particular interest to biologists with high coverage, low chimera rate, and extremely low memory usage compared with exiting gene assembly tools. Moreover, it is naturally compatible with parallel computing platforms. -
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SampleSpecificDBGenerator
Generates custom UniProt-XML databases from RNA-Seq data
SampleSpecificDBGenerator is a program that takes RNA sequencing data analysis results and translates them into protein database entries that are appended to a UniProt-XML file. This XML is condensed, meaning that much of the extraneous author information in UniProt-XMLs is removed for faster search times in Morpheus. Please cite http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00817. -
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Sequence.js
The responsive CSS animation framework for creating unique sliders
Sequence.js is a responsive CSS animation framework created for building interactive sliders, presentations, banners, and other step-based web applications using mostly HTML and CSS. Instead of relying heavily on JavaScript animation logic, the framework controls transitions through CSS class states such as seq-in and seq-out, allowing developers to use familiar front-end workflows and native browser rendering capabilities. The project emphasizes flexibility, enabling developers to animate virtually any CSS property without being constrained by rigid templates or predefined transition systems. Sequence.js supports responsive design, touch navigation, hardware acceleration, and optional dependencies like Hammer.js and ImagesLoaded for advanced interaction handling. ...
