Search Results for "seq" - Page 4
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Showing 224 open source projects for "seq"
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ChiPSeqPair
Match Chip-Seq Data with different features
1. Match Chip-Seq Data with different features 2. Match Chip-Seq Data with input data 3. Find Seq information to facilitate download and analysis of Chip-seq data -
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge... -
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The increasing demand of next-generation sequencing (NGS) studies has remarked the necessity of integrated and reliable pipelines to analyse deep-sequencing experiments in an efficient way. We present RUbioSeq+, a stand-alone and multiplatform application for the integrated analysis of NGS data. More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform...
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ImReP
Immune repertoire assembly from RNA-Seq data
ImReP is a tool written in Python programming language (version 2.7) which is designed to assemble CDR3 region sequences from RNA- or TCR-(BCR-)-Seq reads (either single- or paired-end) and provide immune repertoire as a set of clonotypes with their counts. -
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PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution. Documentation: https://sourceforge.net/p/popoolation2/wiki/Main/
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QuickRNASeq
A pipeline for large scale RNA-seq data analysis
We have implemented QuickRNASeq, an open-source based pipeline for large scale RNA-seq data analysis. QuickRNASeq takes advantage of parallel computing resources, a careful selection of previously published algorithms for RNA-seq read mapping, counting and quality control, and a three-stage strategy to build a fully automated workflow. We also implemented built-in functionalities to detect sample swapping or mislabeling in large-scale RNA-seq studies. Our pipeline significantly lifts large... -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base... -
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Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial
RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal... -
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MaxInfo
Transcriptome assembler for RNA-seq
MaxInfo is an automated transcript discovery and quantification software designing for high-throughput RNA sequencing (RNA-seq). Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
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ROP : Read origin protocol
ROP is a computational protocol to discover the source of all reads
... output by our method is not limited to RNA-Seq technology and may be applied to whole-exome and whole-genome sequencing. For more details see: https://sergheimangul.wordpress.com/rop/ ROP Tutorial: https://github.com/smangul1/rop/wiki -
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EpiMINE
program for mining epigenomic data
EpiMINE is a program designed for mining epigenomic data. This application performs genome wide based quantitative and correlative analysis between different annotated or raw chip-seq like datasets in the regions of interest (RI). Apart from this the tool takes the advantage in linking results with expression data. It is available both in graphical user interface and in command line form. It can be executed in Mac and Linux platforms. Dependencies: python >= 2.7 version python packages... -
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ngs-suite
A set of NGS tools for DNA-seq and BS-seq
ngs-suite aims is to collect a set of fast and well written C++11 software to handle analysis and manipulation of NGS short reads. It works with DNA-seq and BS-seq data. -
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
16S rRNA amplicon analysis and shotgun metagenome sequencing are two main culture-independent strategies to explore the genetic landscape of various microbial communities. 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... -
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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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PeaksAndValleys
Peaks and Valley detection using NGS data
Active regulatory elements in eukaryotic genomes are typically associated with nucleosome-depleted regions that are hypersensitive to digestion by nonspecific endonucleases. Techniques which distinguish active regulatory elements by virtue of this include micrococcal nuclease digestion of chromatin (MNAse-seq), which preferentially depletes DNA which is not tightly bound by proteins, and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq), which enriches for sequences which... -
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ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing... -
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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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... 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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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... -
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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... -
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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/...