Search Results for "miarma-seq" - Page 4
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Showing 225 open source projects for "miarma-seq"
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fourSig
Analyze 4C-seq data.
fourSig is a suite of programs for analyzing and visualizing 4C-seq data. -
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Crosshub
Multi-way analysis of The Cancer Genome Atlas (TCGA) project datasets
Crosshub enables multi-way analysis of RNA-Seq, miRNA-Seq and methylome data of The Cancer Genome Atlas (TCGA) project: 1. differential expression analysis (genes, alternative transcripts and miRNA) 2. regulatory miRNA prediction (TargetScan, DIANA microT, mirSVR, PicTar, miRTarBase + co-expression) 3. regulatory TF prediction (ENCODE ChIP-Seq + co-expression) 4. methylation profiling analysis 5. -
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CSBB-v2.0
Computational Suite for Bioinformaticians and Biologists
...CSBB is currently available on Linux, UNIX and Windows platforms. Currently CSBB provides 16 modules focused on analytical tasks like normalization, visualization, statistics, RNA-SEQ etc. -
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SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
SnowyOwl is a gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions, and to evaluate the resulting models. The pipeline has been validated and streamlined by comparing its predictions to manually curated gene models in three fungal genomes, and its results show substantial increases in sensitivity and selectivity over previous gene predictions. -
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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. ... -
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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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...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 these common tasks. RUbioSeq+ is free and includes all the core functionalities implemented in the original release of RUbioSeq (v3.2.1) but, also, outperforms and expands RUbioSeq capabilities supporting the parallelized analysis of full genomes in computing farms. ...
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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. -
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wechat4u.js
JavaScript implementation of WeChat wechat web interface
...Fix some data in Contact and Message data is not enumerable. Pass the complete Error object to the upper-level code, and put the original Chinese error description in err.tips. The bot.getContact(Seq) method adds the Seq parameter to support incremental acquisition of complete contacts. -
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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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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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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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ROP : Read origin protocol
ROP is a computational protocol to discover the source of all reads
...ROP profiles repeats, circRNAs, gene fusions, trans-splicing events, recombined B/T-cell receptor sequences and microbial communities. The ‘dumpster diving’ profile of unmapped 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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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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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 are nucleosome-depleted. These techniques are especially advantageous due to their limited requirements for reagents, and advances in next-generation sequencing technologies have made them increasingly useful for assessment and identification of novel regulatory elements. ... -
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RNAseq Tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud
rnaseq_tutorial is a tutorial and educational resource created by the Griffith Lab that guides users through the steps of RNA-seq data analysis. It includes working pipelines for alignment, differential expression, alternative splicing, visualization, and interpretation. It is designed to run in the cloud or local environments, providing introductory material on file formats, reference genomes / annotation, QC, mapping, quantifying expression, visualizing results, etc. -
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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: rpy2(v2.8.1), pysam(>0.8.4), pybedtools(v0.7.7) and wxpython (only for GUI form) R with following packages: gplots, ggplot2, RColorBrewer, FactoMineR, kernlab, bnlearn, igraph, fastcluster, caret and ROCR bedtools (2.16/2.17/2.25) Manual & different forms of EpiMINE can be downloaded is available under "Browse Files" section For any help, you can reach us at epimine.help@gmail.com -
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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? -
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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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ISVASE
identification of sequence variant associated with splicing event
...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 with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time. -
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...QuickMIRSeq is a powerful and flexible open source tool for accurate 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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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. -
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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
...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.
