Search Results for "rna" - Page 4
Sort By:
Showing 135 open source projects for "rna"
View related business solutions-
Stay productive working at any distance from anywhere with Monitask.
-
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.
-
1
CAPE RNA
Classification based Analysis of Paired Expression data of RNA
CAPE RNA is package of command-line tools for integrated analysis of miRNA-mRNA expression data. miRNA-mRNA interaction states are assigned for each sample independent of a priori known experimental groups. Using these interaction classifications Jaccard-indexes are calculated to evaluate the quality of a predicted interaction based on the distribution of assigned interaction states compared to experimental groups. In addition, negative correlation between miRNA and mRNA expression can... -
2
StatAlign
An extendable statistical multiple alignment tool.
StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny on a single... -
3
MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
4
Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
DEW is a platform that allows users to explore RNA-Seq data. A web-based Graphical User Interface is included. The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization algorithm... -
Boost application security and continuity with SKUDONET ADC, our Open Source Load Balancer, that maximizes IT infrastructure flexibility. Additionally, save up to $470 K per incident with AI and SKUDONET solutions, further enhancing your organization’s risk management and cost-efficiency strategies.
-
5
Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
6
A Scalable Multicore Code for RNA Secondary Structure Prediction
-
7
deFuse is a software package for gene fusion discovery using RNA-Seq data. deFuse .tar.gz bundles will be released periodically on the sourceforge site, see Files. Questions can be posted to the sourceforge discussion forum. The sourceforge wiki is depracated in favour of documentation included with the package. Development of deFuse is on the bitbucket site, linked below.
-
8
FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.
-
9
VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
It protects your internal resources such as behind-the-firewall applications, teams, and devices.
-
10
Jenotator
Jenotator - Java Genome Annotation and Analysis Tool for DNA and RNA
Jenotator - Java Genome Annotation and Analysis Tool for DNA and RNA -
11
FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi... -
12
Tag-find
a python script to recognize specific sequence of tags
Tag-find is a python script developed to clean up reads from a specific 12 nucleotides long tag sequence used during the cDNA library preparation for RNA-seq experiments. -
13
GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
Note: This version requires additional SQLite database files. Contact the developers to obtain them. Use http://www.integrativegenomics.org/ for the latest data and analyses. GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser. Input - any genome-wide data data in .bed format... -
14
Dress Up RNA seq
End-to-end automated pipeline of RNA seq packages for an HPC system
The purpose of DressUp is to create an end-to-end RNA seq pipeline in which all of the steps of analyzing data from an Illumina sequencer is done in one step in an HPC environment. RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs... -
15
Tuque
Tools for mapping RNA-Seq reads to eukaryotic genomes
Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals -
16
Webapp
A web interface to the SnowyOwl gene prediction pipeline
-
17
SpeedyQuant
Quantifies DNA, RNA or protein bands in agarose or acrylamid gels.
SpeedyQuant is a gel imaging/analysis software that automatically detects and quantifies gel bands (DNA, RNA, protein) in agarose or acrylamid gels. When calculating the relative strength of each band (% of most prominent band) it takes the background noise into account. This leads to accurate and comparable results. Several options can be used to tune the detection process. Here we provide the source code of the program (Perl script) that can be run on any OS with Perl installed (e.g... -
18
rnasimulase
Simulation of allele-specific RNA-seq data
Simulation of allele-specific RNA-seq data -
19
Onco-STS
A web-based Laboratory Information Management System
Onco-STS is a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. The systematic sequencing and analysis of tumour samples, as well other oncogenomic experiments, necessitates the tracking of relevant sample information throughout the investigative process. These meta-data of the sequencing and analysis procedures include information about the samples and projects as well as the sequencing centers, platforms, data locations, results... -
20
ViNSS View
Vienna Notation Secondary Structure Viewer
ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing. -
21
-
22
NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
23
Altrans
Quantification of Splicing Events
Altrans is a method for the relative quantification of splicing events. It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome. It uses paired end reads where one mate maps to one exon and the other mate to a different exon and/or split reads spanning exon exon junctions to count “links” between two exons. When there are overlapping exons, these are grouped into “exon groups” and unique portions of each... -
24
Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data. -
25
RNAseqR
RNA-seq expression analysis tool
RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems. With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by Stekel, et...