Search Results for "linux script"
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Showing 42 open source projects for "linux script"
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Th3inspector
Best Tool For Information Gathering
...It exposes a single command-line entrypoint (Th3inspector.pl) with many switches for common reconnaissance tasks — examples include website info, whois, MX lookup, geo-IP, subdomain discovery, CMS detection, port scanning, and Cloudflare real-IP resolution — so a user can chain many checks from one script. The project provides simple install wrappers for Linux, Android/Termux and even instructions for Windows (Perl + CPAN modules), and includes helper scripts to update or install dependencies automatically. The repository is actively packaged as versioned releases in the README (current noted version 1.9) and is distributed under an MIT license. -
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MANTI
MANTI - Mastering Advanced N-Termini Interpretation
MANTI is a one-stop shop N-termini annotation & evaluation solution. MANTI was previously (un)known as muda.pl ahead of v3.7, the project was renamed to MANTI.pl with v3.7 on 2019-06-24. It congregates information from different MaxQuant or DiaNN/MSFragger output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data congregation is the modificationSpecificPeptides.txt or diann-output.pr_matrix.tsv file - additional data is inferred... -
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autoplot
Simple Gnuplot automation and plot conversion tool.
Autoplot is a simple Perl script to plot Gnuplot files with simple dependency checking and conversion of the plots to different formats using rsvg-convert. The Gnuplot scripts must plot to a SVG terminal and output the result to STDOUT for the script to work as intended. The script reads all .gnuplot files in the working directory and creates SVG plots from them in svg subdirectory. SVG plots can be converted to PDF and PNG format, while the resulting files are placed in pdf and png... -
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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... -
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MANTI.pl / muda.pl
muda.pl - MQ unified data assembler
-------- ATTENTION START: RENAMING muda.pl was renamed to MANTI.pl with v3.7, project development can be tracked on the MANTI project page on sourceforge.net. Old versions remain here for archival purposes. -------- ATTENTION END muda.pl is an evaluation script (written in Perl) without great dependencies. It congregates information from 4 different MaxQuant output files into a master file suitable explicitly for protein neo-termini analyses. The central anchor for the data... -
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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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CNVision
CNV prediction from Illumina genotyping data
CNVision is a Perl script that runs Illumina genotyping data (all chips from 300k to latest Omni) through PennCNV, QuantiSNPv2.3 and GNOSIS (an in-built algorithm). It merges the results and assesses the quality of the raw data. CNVision can also identify de novo CNVs in family-based data using a highly accurate algorithm that considers the possibility of CNVs in either parent based on the raw genotyping data. The script is optimized to work in a UNIX-based environment; it should work in... -
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MethylExtract
High-Quality methylation maps and SNV calling from BS-Seq experiments
MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources: sequencing errors, bisulfite failure, clonal reads and single nucleotide variants. MethylExtract detects variation (SNVs – Single Nucleotide Variation) in a similar way than VarScan, a very sensitive method extensively used in... -
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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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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
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parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A...
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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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CPU Balance
User-based CPU quota tool
CPU Balance is a Perl script to balance the CPU usage among users. It will allocate CPU resource to each user equally only by the command renice, no matter how many processes/threads a user runs. ################ # Basic Renice Goal ################ 1. User-based balance: every user get the same cpu percentage if they ask for more; 2. all the jobs of one user has the same NI; 3. NI of all jobs tend to move as large as possible when balanced; 4. No sudden change on NI. max... -
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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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A batch primer selection program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. BOSS will select oligos for gap closure of both contig and scaffold gaps. See readme for details.
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Byte Investigator
Scripts for parsing and general use in Computer Forensics - Octane Lab
O projeto Byte Investigator do Octane Labs nasceu com a finalidade de se ter um kit de ferramentas (scripts perl) de parsing de varias estruturas do ambiente Windows (arquivos e estruturas dos file systems). Estas ferramentas poderão ser utilizadas no cotidiano dos profissionais e pesquisadores de segurança nas tratativas de resposta a incidentes de Segurança de Informação e Computação Forense. A técnica de parser ou parsing consiste em usar um programa que detalhe as informações contidas em... -
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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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BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
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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.
