Search Results for "learning linux command line" - Page 2
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Showing 634 open source projects for "learning linux command line"
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genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the... -
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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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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
September 2021: the code repository has migrate to https://github.com/UWPR/Comet Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab... -
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SpectralWorks
View, manipulate, analyze (LS fit, SVD, FT), and make figs of, spectra
Program for viewing, editing, manipulating, and analyzing absorbance spectra. Simple arithnetic includes making linear combinatins of up to 10 spectra. Advanced functions include fitting spectra as LC of standard basis spectra, singular value decomposition, Fourier transform, differentiation, integration, global fitting of 3D titration and kinetic data. Graphics features allow composing Figures and export to postscript files which can be converted to pdf, imported into photoshop for... -
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miRPV
miRPV: An automated pipeline for miRNA Prediction and Validation in si
miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence. System Requirement CPU: AMD64 (64bit) Memory: 2Gb RAM Storage: 5Gb Ubuntu 18.04 -
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sdsorter
Easy manipulation of sdf molecular data files.
sdsorter provides convenient routines for manipulating the contents of sdf molecular data files based on the embedded sd tags. -
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MiModD
Mutation Identification in Model Organism Genomes using Desktop PCs
MiModD is a software package for genomic variant identification from next-generation sequencing (NGS) data with optimized usage of system resources and a user-friendly interface. For most model organism genomes it lets the user carry out a complete analysis from unaligned genomic NGS read data to an annotated list of variants on a regular Desktop PC within a few hours. Its user-interface is beginner-friendly and designed to encourage geneticists to analyze NGS data themselves without the... -
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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Red Hat Enterprise Linux on Microsoft AzureRed Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
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'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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hr ("High Resolution") is a small command-line utility to calculate possible elemental compositions for a given mass. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite
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ASGARD
Metabolic reconstruction from DNA or protein sequences.
ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS. -
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MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
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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... -
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MitoSAlt
Identification of mitochondrial structural alterations
MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided. -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
GenSeed-HMM is a program for seed-driven progressive DNA assembly. It differs from the previously published GenSeed in many aspects, but more pointedly by being able to use an HMM profile as seed. Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated... -
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slimfastq
An efficient lossless compression for fastq files.
slimfastq is a cli application that compresses/decompresses fastq files. It features: * High compression ratio * Relatively low cpu/memory usage * Truly lossless compression/decompression -
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Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.
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ModST
A tool to search post-translational modifications in a blind mode
ModST (pronounced as modest) is a tool to search post-translational modifications (PTMs) in mass spectrometry data in an unrestrictive manner. It can search for hundreds of modification without any user provided information for variable modifications. Due to data level parallelization implemented through perl it is fast, portable and easy to use to identify and analyse PTMs in MS/MS data. -
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This project hosts a library and tools for sharing simulation experiments encoded using SED-ML.
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IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Please cite: Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. LNBI. 4463:394-405.
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fas2svg
Visualize genetic code structure from fasta file.
Generate svg file from fasta file. -
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MPI-dot2dot
A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters
MPI-dot2dot is a parallel tool to accelerate the identification of Tandem Repeats on multisequence datasetes. This tool receives as input a multisequence file with FASTQ or FASTA formats. It uses MPI processes and OpenMP threads to exploit the compute capabilities of multicore clusters.