Search Results for "perl script"
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Showing 25 open source projects for "perl script"
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IMS Open Corpus Workbench
Indexing and query tools for very large text corpora
The IMS Open Corpus Workbench is a collection of tools for managing and querying large text corpora (100 M words and more) with linguistic annotations. Its central component is the flexible and efficient query processor CQP, which can be used interactively in a terminal session, as a backend e.g. from a Perl script, or through the Web-based GUI CQPweb. -
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
...The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred from different other source files from the corresponding folder. Maybe also useful for normal proteomics purposes but this script is heavily optimized for protein neo-termini identification and validation. A graphical interface is available as Yoğurtlu_MANTI (a Perl/Tk script) + execut. application versions for Win1x without the need to have Perl installed locally. For a very detailed explanation of script parameters and the evaluation strategy, please consult the extensive manual PDF -
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PINCIS
PINCIS.pl is a Perl bioinf. script to analyze PICS data
PINCIS.pl (PIcs N-/C-terminal Inferred Substrates perl script) is a small, command line tool to designate and analyze PICS (Schilling et al., Nat. Protocols, 2011) data to gain the prime and non-prime site specificity of proteases. Thus, the script filters given peptide lists for library peptides (generated by the digestion protease in the proteomics workflow rather then the protease of interest) and prints out lists of inferred N- and C-terminal cleavage window extensions which can be concurrently used to generate cleavage specificity visualizations like the iceLogo (https://iomics.ugent.be/icelogoserver/create). -
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MANTI.pl / muda.pl
muda.pl - MQ unified data assembler
...Maybe also useful for normal proteomics purposes but this script is heavily optimized for protein neo-termini identification and validation. For a more thorough explanation of script parameters and evaluation strategy, please consult the extensive manual PDF. -
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Print the English name of a number of any size. Number can be run on the command line, or as a CGI script. Number prints names in both the American and European naming system. Number can also print the decimal expansion of a number.
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q pipeline manager
q: integrated platform for pipeline configuration and management
The q utility is a platform for creating and managing data analysis pipelines. It expands the value of your existing job scheduler - either Grid Engine or TORQUE PBS - through numerous functions that help you organize, submit, monitor, manage and share your informatics work. Data processing pipelines require high-level organization and parallelization of work to optimize resource utilization and decrease the time to results. q (from queue) allows complex job sequences to be efficiently... -
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FastAlign.pl
FastAlign is a perl script which uses the heuristic method of tfasty
FastAlign.pl provides a more intuitive output to find exon-intron junctions. The query string is in amino acids and the hit string is in nucleotides. There are extra nucleotides at the end of the hit string (option -diff and by default = 10), that allow to verify if the intron start with common rules (5'-GTGCGA-... for group II intron and after an exonic T for group I intron). If you have Emboss, you can genarate a graphic with option -graph 1. Dependencies: - Perl - Bioperl - UNIX... -
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latexdiff is a Perl script, which compares two latex files and marks up significant differences between them (i.e. a diff for latex files). Various options are available for visual markup using standard latex packages such as "color.sty".
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ReferenceFree
Scripts for reference free genomic analysis
These are Python scripts plus C/C++ programs for automating the reference free genomic analysis described in: Kua C-S, Ruan J, Harting J, Ye C-X, Helmus MR, et al. (2012) Reference-Free Comparative Genomics of 174 Chloroplasts. PLoS One 7(11). http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0048995 Analytical concept conceived by CHCannon and CSKua. Original script written in Mathematica by CHCannon. -
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RICmerge
Improved Isobaric Label Reporter Ion Assignment
This script and underlying data are in support of the manuscript entitled "Improved reporter ion assignment of raw isobaric stable isotope labeled LC-MALDI-TOF/TOF MS/MS spectral data for quantitative proteomics". Authors: Thomas Jakoby, Andreas Tholey and Bart H.J. van den Berg* * = corresponding author bvdberg@live.com -
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this script is to visualize the coordinates data. the input is ncbiblast tabular format or a simple coordinates file. output is a png graph file
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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
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Protein ALignment Optimiser (PALO) is a script for the selection and alignment of the best combination of transcripts among orthologous genes. PALO is mainly written in Python, although other programming languages are also implemented (R, Perl...).
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Byte Investigator
Scripts for parsing and general use in Computer Forensics - Octane Lab
...Byte Investigator The Byte Investigator project from Octane Labs was born in order to be a parsing toolkit for several Windows structures (files and file system structures). These Perl script tools are useful tools for Computer Forensics professionals and Information Security researchers. -
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t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.
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Based on the Buckwalter Morphological Analyzer (Version 1.0) for doing Arabic stemming and POS tagging. Includes a rewrite of the original Perl script, with better documentation and more flexible options, and a C++ interface (usable as a library or app).
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A perl script that converts Illumina qseq files into Phred fastq files for use in Maq. Originally written by Tyler Bachman from UC Riverside, adapted by Eugene Goltsman. Freely available under the terms of GNU GPLv3.
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Stance is a perl script for generating random sentences in Dutch, which can be used as translation exercises for students of Dutch. In its finished version, it should be able to generate only gramatically correct sentences.
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The Simple, Scalable, Script-based Science Processor for Measurements (S4PM) is a system for highly automated processing of science data, scalable up to large processing systems and scalable down to small, special-purpose processing strings.
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unPIC is a Perl script that disassembles Microchip microcontroller's HEX files. This is a powerful tool for all reverse engeneers that creates a well understandable assembly source from a binary file. Creates xrefs, labels, subroutines and much more...
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Phyloview is a perl based CGI script for visualizing taxonomic properties of protein phylogenetic trees.
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The Scenario Data Selector is a Perl script that serves up scenario data on the web. Users can browse data and choose to show by value or as growth rates or indices. Data can be shown by region or indicator - the script takes care of regional aggrega
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For interactive clustering and visualization, Cluster and TreeView by Mike Eisen are great. XCluster by Gavin Sherlock solves the problem of clustering large numbers of files. Now slcview allows you to script generation of cluster and tree images.
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Bobware tool suite is a set of small EDA tools which are useful in the design of integrated circuits. The suite contains a perl/tk script for region planning large ASICs (application specific integrated circuits.)
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