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Showing 18 open source projects for "find"
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CodonU
A python project for analysis of codon usage for gene or genome analys
...This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics research! Find more at: https://github.com/SouradiptoC/CodonU Documentation link: https://souradiptoc.github.io/CodonU Example Link: https://github.com/SouradiptoC/CodonU/tree/master/Examples -
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FusionCatcher
Somatic fusion-genes finder for RNA-seq data
...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, CIC fusions, DUX4 fusions, CRLF2 fusions, TCF3 fusions, etc. - to be as automatic as possible (i.e. the FusionCatcher will choose automatically the best parameters in order to find candidate fusion genes, e.g. finding automatically the adapters, building the exon-exon junctions automatically based on the length of the input reads, etc.) while providing the best possible detection rate for finding fusion genes. -
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GASiC
Genome Abundance Similarity Correction
...GASiC is a method to correct read alignment results for the ambiguities imposed by similarities of genomes. It has superior performance over existing methods. You can find the accompanying paper here: http://nar.oxfordjournals.org/content/41/1/e10.short Thanks to the great work of the SeqAn team, you can now use GASiC as a Knime workflow: https://github.com/seqan/knime_seqan_workflows/tree/master/metagenomics_gasic_workflow -
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fitGCP
Fitting genome coverage distributions with mixture models
...Besides commonly used distributions, fitGCP uses distributions tailored to account for common artifacts. The mixture models are iteratively fitted based on the Expectation-Maximization algorithm. Please find the accompanying paper here: http://dx.doi.org/10.1093/bioinformatics/btt147 -
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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. -
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dna-barcode
Find and analyze barcodes in DNA sequence files
Find and analyze barcodes in DNA sequence files -
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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 -
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AMBIENT
Find active modules in metabolic networks using high-throughput data
...If you wish to use the version used in the paper it is v0.6.3, however I recommend using the latest version which works in the same way but with additional options and has stability and performance improvements. Thanks for your interest! AMBIENT (Active Modules for Bipartite Networks) is a Python module that uses simulated annealing to find areas of a metabolic network (modules) that have some consistent characteristic. AMBIENT does not require predefined pathways and gives highly specific predictions of affected areas of metabolism. For example, scores for reactions based on transcriptional data of their annotated encoding genes can be used in the network and modules of coordinated expression changes can be found. ... -
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The PyCogent project is moving to GitHub. When completed, you will find us at http://github.com/pycogent/pycogent/. You can find the PyCogent website at http://www.pycogent.org.
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CoNIFER
Homepage for CoNIFER (Copy Number Inference From Exome Reads)
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. -
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The QIIME project has moved to GitHub. You can now find us at http://github.com/qiime/. As always, you can find the QIIME website at http://www.qiime.org.
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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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Flow Investigation using N-Dimensions (FIND) is a program designed for analysis and visualization of Flow Cytometry data. FIND focuses specifically on automated population discovery (clustering) methods. The project targets both users and developers.
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PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website: http://www.pymol.org/
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FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra
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RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit against the evolutionary group that the HMM models, and it does this using through iterative database searches and incremental subsequent adaptation of the seed set.
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PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
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A lightweight, browsing-based, 100% Python, federated data integration framework. Users may create custom schemas for disparate sources, query and expand results across sources to find related data; for use in fields such as bioinformatics and datamining
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