Search Results for "content analysis"
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Showing 13 open source projects for "content analysis"
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ViReMa
Viral Recombination Mapper
...Feb 2014 - Our paper (Open Access) is available at Nucleic Acids Research: "Discovery of functional genomic motifs in viruses with ViReMa–a Virus Recombination Mapper–for analysis of next-generation sequencing data" http://nar.oxfordjournals.org/content/42/2/e11 This is an on-going project and updates will be regularly posted. Please get in touch with any questions, problems or suggestions. -
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HCS Analyzer
High Content Screening Analyzer
HCS Analyzer is an open source software dedicated to High Content Screening data processing and analysis. -
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Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
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MethyMer
Design of specific primer combinations for bisulfite sequencing
MethyMer is a Python-based tool aimed at selecting specific primers for amplification of complete CpG islands. These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc. MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome). It also incorporates TCGA CpG methylation... -
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EXCAVATOR2tool
Enhanced tool for detecting CNVs from whole-exome sequencing data
...EXCAVATOR2 is a collection of bash, R and Fortran scripts and codes that analyses Whole Exome Sequencing (WES) data to identify CNVs. EXCAVATOR2 enhances the identification of all genomic CNVs, both overlapping and non-overlapping targeted exons by integrating the analysis of In-targets and Off- targets reads. EXCAVATOR2 can be effectively employed for the identification of CNVs in small as well as large-scale re-sequencing population and cancer studies. EXCAVATO2 paper: http://nar.oxfordjournals.org/content/early/2016/08/09/nar.gkw695.full?keytype=ref&ijkey=O8r64Qj81gfMzLo -
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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. A... -
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Combenefit
Synergy analyses of drug and other other agent combinations
Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Please cite as: "Di Veroli,G.Y. et al. (2016) Combenefit: an interactive platform for the analysis and visualization of drug combinations. Bioinformatics." (http://bioinformatics.oxfordjournals.org/content/early/2016/05/27/bioinformatics.btw230.abstract) Current version (2.021): https://sourceforge.net/projects/combenefit/files/Combenefit%202.02%20WIN_64%20%28PREFERRED%29/ Older version for 32-bit os: https://sourceforge.net/projects/combenefit/files/WIN_32/ Quick user's guide: https://sourceforge.net/projects/combenefit/files/Combenefit_v2.02_quick_guide_v1.03.pdf/download Examples: https://sourceforge.net/projects/combenefit/files/Examples/ Template file: https://sourceforge.net/projects/combenefit/files/REPLICATE_TEMPLATE.xls/download -
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Maximum Common Genome Alignment (MCGA)
Pipeline for creating core genome alignments for phylogenetic analysis
Maximum Common Genome Alignment (MCGA) Tool MCGA is a bioinformatics analysis tool written in Python for generating core genome alignment for bacterial whole genome sequences which can be used to construct phylogenetic trees. -
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GASiC
Genome Abundance Similarity Correction
One goal of sequencing based metagenomic analysis is the quantitative taxonomic assessment of microbial community compositions. However, the majority of approaches either quantify at low resolution (e.g. at phylum level) or have severe problems discerning highly similar species. Yet, accurate quantification on species level is desirable in applications such as metagenomic diagnostics or community comparison. -
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miRNA Temporal Analyzer (mirnaTA)
Differential expression analysis tool for miRNAs in temporal studies
The microRNA Temporal Analyzer (mirnaTA) is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies. It is implemented in Perl and R package (>= 2.13.0) and can be run across multiple platforms such as Linux, Mac and Windows. The mirnaTA requires that users provide data from a minimum of two time points and analyze up to 20 time points. To normalize data and remove technical variability, Normal Quantile Transformation (NQT) was used, and the... -
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iBRAIN2 Workflow Manager
A system for automated analysis and data handling for RNAi screens
The iBRAIN2 software system for RNAi high-content screening integrates automated analysis and customizable data management. It enables robust and complex parallel processing on computer cluster infrastructure and allows for reliable storage of primary and resulting data sets. -
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Software for making Clusters of Orthologous Groups (featuring the new EdgeSearch algorithm). Latest ref: Kristensen DM, Kannan L, Coleman MK, Wolf YI, Sorokin A, Koonin EV, Mushegian A. Bioinformatics 2010.
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XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.
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