Search Results for "seq" - Page 5
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Showing 268 open source projects for "seq"
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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INTEGRATE: Calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. To download source code, reference manual and test case, please go to 'Files'. Also refer to 'Wiki' for details.
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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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... quantification of known miRNAs/isomiRs. 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/quickmirseq/files/, and are also available online https://baohongz.github.io/QuickMIRSeq/
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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... -
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mirPRo
Tool for miRNA-seq analysis in C++
mirPRo is a tool for miRNA-seq analysis. It can quantify known and novel miRNAs in single-end RNA-seq data and provide useful functions such as IsomiR detection and "arm switching" identification, miRNA family quantification, and read cataloging in terms of genome annotation. mirPRo only works for species that has reference genome. [1] Who are we? Please visit our website http://bioinfolab.miamioh.edu [2] How to cite mirPRo? Shi J, Dong M, Li L, Liu L, Luz-Madrigal A, Tsonis PA, Rio-Tsonis... -
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
.... Consequently, the community will profit from a platform seamlessly connecting detailed visual inspection of RT signatures and automated screening for modification candidates. CoverageAnalyzer was developed in response to the demand for a powerful inspection tool, running on all 3 OSes. With SAM standard as input and an intuitive GUI, even non-experts can accomplish a variety of tasks, from visualization of RNA Seq data, up to sophisticated modification analysis with significance-based candidate calling. -
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QAmiRSeq
A strand aware pipeline for accurate quantification of miRNAs/isomiRs
... to conduct further investigation and discovery. 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.
This code genome accessibility for transcription factor (TF)-binding in Bacteria. 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... -
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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. -
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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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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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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. -
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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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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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Ritornello
Control free ChIP-seq peak caller
Ritornello is a ChIP-seq peak calling algorithm based on signal processing that can accurately call binding events without the need to do a pair total DNA input or IgG control sample. This project has moved to github as follows: https://github.com/KlugerLab/Ritornello -
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The friendly GWAS SNP enrichment tool
Tests for enrichment of GWAS SNPs in epigenetic datasets
... annotations are then supplied as bed files. The program will go through a directory of bed files e.g. all of the encode ChIP-seq datasets. Enrichment is checked against random samples from all the SNPs. The output is a tab delimited text file with the number of target loci hit, the mean number of background loci hit, the fold enrichment and a P value derived from the number of background permutations that hit as many or more loci as the test SNPs, divided by the number of permutations. -
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mRIN
Assessing mRNA integrity directly from RNA-Seq data
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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... -
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scell
single-cell RNA-seq analysis software
SCell is an integrated software tool for quality filtering, normalization, feature selection, iterative dimensionality reduction, clustering and the estimation of gene-expression gradients from large ensembles of single-cell RNA-seq datasets. SCell is open source, and implemented with an intuitive graphical interface. Binary executables for Windows, MacOS and Linux are available at http://sourceforge.net/projects/scell, source code and pre-processing scripts are available from https... -
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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... -
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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... -
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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...