Search Results for "sql command line" - Page 17
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Showing 635 open source projects for "sql command line"
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Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
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This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.
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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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An R package implementation of a consensus clustering methodology. This package allows users to perform re-sampling statistics based clustering using multiple clustering algorithms to assess the robustness of both clusters and members of clusters.
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Suite of software tools for transcription factor binding site search, gene annotation, and orthology filtering. Some tools in the CisOrtho package are required along with MAQ for use in MAQGene.
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Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.
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Algorithm Based Automatic Contiguation of Assembled sequences (ABACAS) is an integrated platform for quickly contiguating reference based assemblies.
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Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)
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The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
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FusionMiner is a molecular biology program which accepts genomic alignments in BLAST/BLAT tabular output and attempts to find true fusion transcripts. A single command runs the pipeline and generates results.
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Small set of utilities used by the 2010 iGEM Mexico-UNAM-CINVESTAV Team to automate biobricks from files
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HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
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This package, for R environment, detects DAE peaks ratio on data gotten from LightCycler instrument.
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Metmask has moved to github http://github.com/hredestig/metmask Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.
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Phylogenetic Representativeness is a method for estimating adequacy of taxon sampling for phylogenetic studies. Through a series of statistics generated by PhyRe, it is possible to evaluate taxon coverage within a given group.
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This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.
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FAS-DPD is a program to design degenerate primers for PCR.
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Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.
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An R package for detailed inspection and analysis of LCMS data. An R package developed by Sukhdeep Singh at Department of Surgery and Cancer, Imperial College London,UK.
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qips is a software package for analyzing ChIP-seq ("Chromatin ImmunoPrecipitation on sequencing") data. It finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.
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Common code developed by researchers in the Edwards Bioinformatics Group at SDSU. This code is free for everyone to use. It is our base code that we provide on an as-is basis. Please let us know if you use the code or have questions/comments
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Given low-density genotypes for pedigrees, and dense genotypes for some people in those pedigrees, computes high-density genotypes for some other people in those pedigrees. This reduces genotyping effort.
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The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
