Search Results for "data extract"
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Showing 10 open source projects for "data extract"
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1
DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
...Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid in discerning differential gene expression across diverse conditions. Computational biology is in need of methods for integration of static networks and gene expression data, since it provides interesting insights into the dynamics of biological systems. DEN is an R/Bioconductor based package designed to assemble different types of human bio-molecular interactions as a complete interactome and contains functions to extract dynamic active networks by integration of gene expression data. -
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Ymap - Yeast Mapping Analysis Pipeline
Pipeline for large-scale genome changes analysis of genome datasets.
...The YMAP pipeline automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other categories of data and other pathogen species with small genomes. -
3
caplib
Correct, translate and analyze combinatorial library sequencing data
Originally developped to handle PacBio CCS data for an AAV capsid library. This program will extract, correct, translate and analyze the sequencng data, starting from the CCS fastq file. -
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AgED
AgED - Analysis given Experimental Data
AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments. -
5
SeqHunter2
a stand-alone bioinformatics software for querying genome sequences
...It is programmed with the following functions: 1) collect and manage local sequence databases; 2) run blast search by using a batch of sequences and with abundant output formats; 3) extract sequences by a set of IDs or coordinates; 4) generate sequences alignment; 5) edit sequence and translate nucleotide to proteins; 6) browse genome and search genes; 7) collect resource items and link to the website. The full version collects all available oomycete plant pathogens genome sequences and information of research related resource, while the lite version is flexible for non-oomycete users to collected the data they are interested. -
6
metaProt
Pipeline to analyze coding regions in metagenomic projects
metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this. -
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Image analysis program that extract the movements of the bacteria from digitised movies and data processing associated.
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8
H-mito is a mitochondrial DNA haplogroup prediction tool based on the phylogenetic tree http://www.phylotree.org/. Ancillary scripts: mitoP.py to extract mutation lists and clustal-2-fasta.zip to join, align through clustalw and convert data.
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9
Program designed to extract scientific names stored in PDF documents located on a web address, entering data into a table with Darwincore format. Additionally this application uses the "FindIT" web service located at http://www.ubio.org.
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10
danaides
Meta data extractor based on ontologies
Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).
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