Search Results for "rna" - Page 4
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Showing 181 open source projects for "rna"
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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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Ericscript is a computational framework to detect gene fusions from paired end RNA-seq data with high sensitity and specificity.
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Protein Expression Control Analysis (PECA) is a statistical software to identify genes subject to significant RNA- and protein-level regulation with control of false discovery rate.
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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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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...
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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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CRISPR-Offinder
a CRISPR guide RNA design and off-target searching to
Summary: Design efficient and specific CRISPR small guide RNAs (sgRNAs) is one of the keys for a successful application of CRISPR technology. Importantly, more and more new RNA-guided endonucleases with different protospacer adjacent motif (PAM) have been discovered. Therefore, there is an urgent need to develop a versatile tool to design sgRNA to satisfy the requirement of different RNA-guided DNA endonucleases. To this end, a flexible sgRNA design program named “CRISPR-offinder” was developed... -
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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... -
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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. It is implemented in C++ with full support of multiple threading, to allow fast... -
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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... -
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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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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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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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IM-TORNADO
Illinois Mayo Taxonomy Operations for RNA Database Operations
IM-TORNADO HAS MOVED TO GITHUB: https://github.com/pjeraldo/imtornado2 Pipeline for analysis of paired-end 16S rDNA amplicon data. -
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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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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... -
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CT-Finder
A Web Service for CRISPR Optimal Target Prediction and Visualization
CT-Finder is a web service that allows a user to upload DNA sequences, set specifications according to experimental goals, and receive candidate guide RNA targets. Optimal candidates are suggested through consideration of predicted off-target effects. A visualization of on-target and off-target matches against the chosen reference genome is provided in JBrowse. [1] Who are we? Please visit our website http://bioinfolab.miamioh.edu [2] How to cite CT-Finder? Zhu, H. et al. CT-Finder... -
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baSeq
A very basic DNA sequence manipulation tool.
Reverse, complement and translate DNA/RNA sequences. Supports all IUPAC ambiguity codes. -
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RNA-DM
RNA Dynamics Miner
Recently, RNA dynamics - the complex conformational transition and hierarchical free-energy landscape of RNAs has been demonstrated to be critical in understanding RNA functions and relevant biological processes. RNA Dynamics Miner (RNA-DM) is a bioinformatics tools desigined to mine the kinetic landscpae for a given RNA sequence or a large RNA dataset. -
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PRIP
RNA-binding residues prediction using structural features
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lncRScan-SVM
A package for lncRNA prediction
The package is used to classify protein coding and long non-coding RNA (lncRNA) transcripts using support vector machine (SVM). -
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This project aims to provide bit-parallel based string comparison tools on modern accelerators, as well as on common multi-core CPUs. Fundamentally, these tools are specified for biological data (i.e DNA, RNA sequences), however, they could also be extended to process other types of text data.
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SplicingTypesAnno
Annotation tool for alternative splicing types by RNA-Seq data
This package annotates four major splicing types by RNA-Seq data, including intron retention, exon skipping, alternative donor site, and alternative acceptor site. As a post-processing tool for alignment files, it annotates the alternative splicing types with details at the intron or exon level.