Search Results for "rna"
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Showing 71 open source projects for "rna"
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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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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome... -
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BBMap
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
When it comes to cybersecurity, what your clients don’t know can really hurt them. And believe it or not, keep them safe starts with asking questions. With ConnectWise Identify Assessment, get access to risk assessment backed by the NIST Cybersecurity Framework to uncover risks across your client’s entire business, not just their networks. With a clearly defined, easy-to-read risk report in hand, you can start having meaningful security conversations that can get you on the path of keeping your clients protected from every angle. Choose from two assessment levels to cover every client’s need, from the Essentials to cover the basics to our Comprehensive Assessment to dive deeper to uncover additional risks. Our intuitive heat map shows you your client’s overall risk level and priority to address risks based on probability and financial impact. Each report includes remediation recommendations to help you create a revenue-generating action plan.
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface... -
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SPiCEv2.1
Splicing Prediction in Consensus Element
SPiCE is no longer maintained. To access the tool's predictions, please use SPiP, accessible at : https://sourceforge.net/projects/splicing-prediction-pipeline/ or https://github.com/raphaelleman/SPiP If you have questions, please contact me to: r.leman@baclesse.unicancer.fr or raphael.leman@orange.fr v2.1.5 (05/2019) + corr (01/2020): Fix bug for linux version v2.1.4 (03/2019): Proxy management (only for Windows version) v2.1.3 (07/2018): correction bug for first 3' ss import vcf... -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi can be downloaded from the site (https://sites.google.com/site/haithamsobhy/software). Please, do not hesitate to contact Dr. Haitham Sobhy if you need help. Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR... -
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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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viRome
R code/package for virus small RNA sequence data
Please use code here: https://github.com/mw55309/viRome_legacy -
From improving customer experience through seamless sign-on to making MFA as easy as a click of a button – your login box must find the right balance between user convenience, privacy and security.
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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 a... -
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CusVarDB
CusVarDB generated variant protein database from NGS-datasets
CusVarDB is a windows based tool for creating a variant protein database from Next-generation sequencing datasets. The program supports variant calling for Genome, RNA-Seq and ExomeSeq datasets. The program performs mainly 4 modules 1. Align the datasets with reference database 2. Perform the variant calling using Genome Analysis Toolkit (GATK) 3. Annotate the variant using ANNOVAR 4. Create the variant protein database Apart from the main modules, the program also supports additional... -
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TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
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packeis
Check for selection of RNA secondary structure
PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons. -
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mirplant
miRPlant: An Integrated Tool for Identification of Plant miRNA
please cite: An J, Lai J, Sajjanhar A, Lehman ML, Nelson CC: miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data. BMC bioinformatics 2014, 15(1):275. We will create index for you if you tell us your interested plants (j.an@qut.edu.au). -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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gogadget
A toolbox for interpretation and visualization of RNA-seq GO analysis
gogadget is an R package, and can help with the visualization and interpretation of GO enrichment analysis of RNA-seq data. It is developed especially for the use in combination with goseq. The functions that are available in this package are extensively described in the user's guide. To install the package download the "gogadget_2.1.tar.gz" file, open R and install with the following line: install.packages( "C:/your/directory/gogadget_2.1.tar.gz", repos = NULL, type="source") The package... -
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siFi21
si-Fi is a Software for RNAi (RNA interference) off-target prediction.
si-Fi is a Software for RNAi (RNA interference) off-target prediction The software is designed for checking long-double stranded RNAi constructs for target specificity and silencing efficiency. It can be used also to select sequence regions suitable for designing RNAi constructs. The program provides clear tabular and graphical outputs. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
CRISPR/Cas system undoubtedly holds great potential for genome editing. Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the... -
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faif
C++ header only library with AI and bioinformatics algorithms
C++ header only library, small and fast; Naive Bayesian Classifier, Decision Tree Classifier (ID3), DNA/RNA nucleotide second structure predictor, timeseries management, timeseries prediction, generic Evolutionary Algorithm, generic Hill Climbing algorithm and others. -
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MELTING is a software to compute, for a nucleic acid duplex, the enthalpy and the entropy of the helix coil transition and then the melting temperature. Four types of hybridization are possible : DNA/DNA, RNA/RNA, RNA/DNA and mRNA/RNA.
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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. RNA-Seq vs. clinical (TNM, stage, follow-up) correlation analysis Generates Excel summaries... -
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CircularLogo is a light-weighted, easy to use web application that visualizes the intra-motif dependencies of a DNA or RNA motif.
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BioFace is simple software for editing and analyzing DNA, RNA, and protein sequences that is written in Java using SWT and JFace as libraries. Opening GenBank, FASTA, EMBL, or simple sequence files and analizing these sequences can be done.
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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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CoverageAnalyzer
RNA modification detection by RT signatures in deep sequencing data
Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures relying on both, sequence dependent mismatch patterns and RT arrests. Common alignment viewers lack in specialized functionality, such as filtering, tailored visualization, differential analysis and export...