Search Results for "per linux"
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Showing 13 open source projects for "per linux"
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In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and... -
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guglinatts-it
Guglina TTS, edizione speciale: in italiano (guglinatts-it)
Guglina TTS, edizione speciale: in italiano (guglinatts-it), è un sintetizzatore vocale originariamente progettato per il portoghese brasiliano. Utilizza l'API di sintesi vocale di Google Traduttore. Leggi gli screenshot per gli ipovedenti. Trasforma il testo in audio, consentendo a persone non vedenti o ipovedenti di accedere al contenuto visualizzato sullo schermo. Sebbene il pubblico di riferimento principale per i sistemi di conversione da testo a voce - come Guglina TTS IT - sia... -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
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Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
Sofware for reference-based transcriptome reconstruction. It performs reconstruction starting from short reads obtained from RNA-seq. It is best suited to manage the transcriptomes of lower eukaryotes with a low number of introns per gene and it can be used also for procariotes. It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. It provides in output the positions of the transcripts identified,... -
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Digital Expression on the Web
DEW is a platform that allows users to explore RNA-Seq data
DEW is a platform that allows users to explore RNA-Seq data. A web-based Graphical User Interface is included. The analysis proceeds as such: gapped alignments are performed and corrected for length, PCR and fragment bias so that a Fragment Per (effective) Kilobase per Million of reads (FPKM) is estimated as well as the simpler Reads Per Kb per Million of reads (RPKM). When provided with multiple isoforms and in the ‘contextual’ mode, corrections include a expectation maximization... -
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Average
Command-line calculator of basic statistics.
Average is a simple and fast command-line Perl utility for calculating basic statistics on a list of numbers (one number per line). It works as a traditional Unix filter and can be used as part of those greatly useful chains of piped commands. It calculates average (arithmetic mean), standard deviation, median, total sum, minimum and maximum values present, and shows the number of processed numbers. Entry can by a text file (any column can be specified, default is the first) or... -
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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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Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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ParaSim
Parallelized calculation of molecular similarities
Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently... -
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A set of Unix command line tools for quick and convenient batch processing of tabular text files (a.k.a., tab-delimited, csv, or flat file format) with a header line. Provides delimiter and compression detection, column reference by name. * tblmap: per-line ("map") computation: derive columns through an expression, delete, reorder, filter rows. * tblred: compute ("reduce") aggregations (e.g., sum, average) over groups defined by key columns. * tbldesc: Summarize columns in file...
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Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals.
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BRMABench is a system of benchmark per comparison. This benchmark makes diverse routines of test in one determined time, the final time expense is always the same and what it determines score it is the amount of interactions in this same time.
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