Search Results for "rna-darts" - Page 2
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Showing 301 open source projects for "rna-darts"
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Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
Fusion gene detection by RNA-seq requires prior setup of several software modules and dependencies which might be troublesome. Furthermore, fusion detection tools tend to report many false positives. Therefore, we developed a detection and filtering workflow bundled into a Singularity container for a streamlined and easy-to-use application. Arriba and FusionCatcher are utilized for fusion calling. Our filtering pipeline uses read counts generated by FeatureCounts and insert size estimation... -
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HipMer
A High performance distributed memory assembler for big genomic data
... and accuracy in metagenomic assemblies. It is able to reconstruct rRNA elements via a separate algorithm which relies on reference SSU and LSU Hidden Markov Models to help traverse the contig graph around ribosomal RNA regions. For more information and publications visit the HipMer Portal (http://portal.nersc.gov/project/hipmer/) MetaHipMer is one component of the ExaBiome project (https://sites.google.com/lbl.gov/exabiome/home), part of the Exascale Computing Project: https://www.exascaleproject.org/ -
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RNA@
RNA annotation tool
RNA@ is a RNA annotation tool for prokaryotic organisms based on a lightened Aho-Corasick like algorithm. The algorithm principle is to encode a data set of nucleotide sequences into a Finite State Machine able to recognize every occurrence of every nucleotide sequence into a genome in a single read of the genome. As nucleotide sequence data set, RNA@ uses a collection of about 300,000 RNA deposited into the NCBI. These RNA are automatically collected from about 25,000 complete deposited... -
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CStone
Short-read de novo assembler that identifies chimeric contigs.
> CStone wiki: https://sourceforge.net/p/cstone/wiki/Home/ Related Software: 1. CStone: (See wiki) 2. CSReadGen: https://sourceforge.net/projects/csreadgen/ 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ -
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CSReadGen
RNA-Seq read simulator that offers a wide range of parameter options.
> CSReadGen wiki: https://sourceforge.net/p/csreadgen/wiki/Home/ Related software: 1. CStone: https://sourceforge.net/projects/cstone/ 2. CSReadGen: (See wiki) 3. CView: https://sourceforge.net/projects/cview/ 4. ChimSim: https://sourceforge.net/projects/chimsim/ 5. TVScript: https://sourceforge.net/projects/tvscript/ -
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miRDP2
Accurately and fast analyzing microRNAs transcriptome in plants
miRDeep-P2 (miRDP2) is developed to accurately and fast analyze microRNAs (miRNAs) transcriptome in plants. It is adopted from miRDeep-P (miRDP) with new strategies and overhauled algorithm. We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA... -
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CIRI
CircRNA Identifier. A de novo circular RNA identification tool
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A new approach to fast data transfer | IBM AsperaIBM Aspera takes a different approach to tackling the challenges of big data movement over global WANs. Rather than optimize or accelerate data transfer, Aspera eliminates underlying bottlenecks by using a breakthrough transport technology that fully utilizes available network bandwidth to maximize speed and quickly scale up with no theoretical limit.
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scDAPA
Detection and visualization of dynamic alternative polyadenylation
... and visualization of dynamic alternative polyadenylation from single cell RNA-seq data. Bioinformatics, 36(4): 1262–1264. https://doi.org/10.1093/bioinformatics/btz701 -
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viRome
R code/package for virus small RNA sequence data
Please use code here: https://github.com/mw55309/viRome_legacy -
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Cell Paint
cellPAINT allows users to create living illustrations of biology.
cellPAINT is a free-form painting app that allows users to create their own living illustrations of cellular landscapes. There are currently several prototypes available: --cellPAINT_coronavirus includes a newly-redesigned user interface, and molecular building blocks for coronavirus, blood plasma, and a simple human cell --cellPAINT_exo includes hand-painted sprites created by Julia Jimenez during an internship, and also allows input of custom sprites through Mesoscope --cellPAINT_VR is... -
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miRSim
Seed-based RNA-Seq Simulator
The miRSim tool can generate the synthetic RNA-Seq data in standard fastq/fasta format by utilizing the sequence-specific properties (i.e., seed and xseed (remaining part of the sequence after removing seed)). Additionally, miRSim also generates the ground truth in CSV format that provides information about genomic location, CIGAR string, sequence, and expression counts. -
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GUIdEStaR: G-quadruplex (GQ) provided by Chariker et al., uORF from uORF-Tools, IRES from IRESbase, Epigenetic modification from Met-DB V2.0 and Choi et al., Small RNA from DASHR 2.0, and Repeats from RepeatMasker For details, please read the main article at https://www.biorxiv.org/content/10.1101/2021.02.25.432957v3
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Lexical Analyzer Generator Quex
Generator of lexical analyzers in C and C++. Unicode Supported.
The goal of this project is to provide a generator for lexical analyzers of maximum computational efficiency and maximum range of applications. This includes the support for Unicode (UTF8, UTF16, ...) and a large variety of other encodings directly and via nested converters such as ICU(tm) and IConv. Sophisticated buffer handling allows to operate on plain file streams, on sockets, or manually fed buffer content. 'Ready-to-build' examples explain related concepts and facilitate practical... -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. The aims of FusionCatcher are: - very good detection rate for finding candidate fusion genes, - very easy to use (i.e. no a priori knowledge of databases and bioinformatics is needed in order to run FusionCatcher), - very good detection of challenging fusion genes, like for example IGH fusions... -
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APAtrap
Identification of APA sites from RNA-seq data
APAtrap - a tool for identification of APA sites from RNA-seq data. [1] APAtrap user manual Please visit the Wiki page of this website. [2] APAtrap Q&A For Q&A, please visit the Blog page of this website. [3] APAtrap bug report You can report a bug as a Ticket request, or start a topic session in the Discussion webpage of this website. [4] How to cite APAtrap? Ye C, Long Y, Ji G, Li Q. Q, Wu X (2018) APAtrap: identification and quantification of alternative... -
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DAMIAN
Identification of pathogenic microorganisms in diagnostic samples
DAMIAN provides capabilities to detect known and novel pathogens in RNA and DNA samples of various sources. It integrates all required processing steps, ranging from the quality control of sequencing reads to the generation of comprehensive reports. The method works for any host organism. -
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Harmony Data Integration
Fast, sensitive and accurate integration of single-cell data
Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq. Harmony has been tested on R versions =4. Please consult the DESCRIPTION file for more details on required R packages. Harmony has been tested on Linux, OS X, and Windows platforms. -
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QuiclickRNAseq
An integrated pipeline for RNA-seq analysis
Quiclick is a python framework for RNA-seq data analysis, including data trimming, mapping, counting and RNA editing analysis. -
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GapFiller
A de novo local assembler for paired reads
GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. GapFiller can be used whenever a sequence is to be assembled starting from reads lying on its ends, provided a loose estimate of sequence length. -
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MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both...
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HyLiTE
Hybrid Lineage Transcriptome Explorer
HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species. Allopolyploidy describes the formation of a new hybrid organism from the union of two or more different parents. Allopolyploid species carry multiple copies of each gene (homeologs), which often exhibit unusual expression patterns. Homeolog expression levels can technically be determined from next generation sequencing data (RNA-seq), but in practice, assigning reads to one...