Search Results for "graph"
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Showing 44 open source projects for "graph"
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Automate contact and company data extractionGenerate leads at scale without building or maintaining scrapers. Use 10,000+ ready-made tools that handle authentication, pagination, and anti-bot protection. Pull data from business directories, social profiles, and public sources, then export to your CRM or database via API. Schedule recurring extractions, enrich existing datasets, and integrate with your workflows.
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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In addition to computing co-expression clusters, Maccu fishes potential co-expressed genes for a given bait set. All results can be further processed via graph-level operations so that we can compare graphs based on different reference data.
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Croizat
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach. -
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GCB_package
Stand-alone version of the Genome Complexity Browser
This application allows observing genome rearrangements in prokaryotic genomes. It provides rearrangements frequencies profiles and genomes graph representation. -
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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Root Phenotyping Suite
Three different software tools for phenotyping plant root images
...The software provides a robust, efficient and accurate means of phenotyping of roots, by detecting individual root tips and classifying them as belonging to a primary or lateral root. RootGraph is a novel, fully automated and robust approach for the detailed characterization of root traits, based on a graph optimization process. The scheme, firstly, distinguishes primary roots from lateral roots and, secondly, quantifies a broad spectrum of root traits. -
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Meraculous-2D
Eukaryotic Genome Assembler
---------------------------------------- IMPORTANT: Meraculous-2D has been superseded by the HipMer assembler, available here: https://sourceforge.net/projects/hipmer/ ----------------------------------------- Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements. Features include: - Efficient k-mer counting and deBruijn graph traversal - Two modes of handling of diploid allelic variation - Improved scaffolding that produces more complete assemblies without compromising scaffolding accuracy. The assembly is driven by a perl pipeline which performs data fragmentation and load balancing, as well as submission and monitoring of multiple task arrays on a GE/SLURM-type cluster or a standalone multi-core server. ... -
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PanOCT
Pan-genome Ortholog Clustering Tool
PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters. -
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Mass Difference Calculator
Mass Difference Calculator with a Graph for MassLynx data
A Mass Difference Calculator with a graph for MassLynx. Bring in a text file with reference masses and then paste in or browse in another file with a list of mass/intensity pairs. Then look at the best matching points and see what the difference between reference and data comes out as. This is a companion app to ResCalc3 -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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TAG
A tool for metatranscriptome assembly using metagenome graph
TAG is a tool for metatranscriptome assembly using de Bruijn graph of matched metagenome as the reference. TAG is an application of a reads mapping algorithm that we developed for mapping of short reads onto a de Bruijn graph of assemblies. A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph. -
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PRIMUS
Pedigree Reconstruction and Identification of a Maximum Unrelated Set
NEW: Download new version with Pedigree Reconstruction at primus.gs.washington.edu This versions is outdated and incomplete. Please visit the new website for the complete version of PRIMUS. We present a method adapted from graph theory that always identifies the maximum set of unrelated individuals in any dataset, and allows weighting parameters to be utilized in unrelated sample selection. PRIMUS reads in user-generated IBD estimates and outputs the maximum possible set of unrelated individuals, given a specified threshold of relatedness. Additional information for preferential selection of individuals may also be utilized. ... -
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RT-alignment
Graph-based time alignment algorithms for multiple LC-MS datasets
...The main challenge in this task lies in correcting retention time shifts, which are inevitable even on the same instrument and under the same elution conditions. For large-scale studies, multiple instruments or multi-week experiments are often required, which exacerbates the problem. We present a new graph-based time alignment algorithm that can align these less similar LC-MS maps, which cannot be effectively handled by existing methods. -
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SplitMEM
Graphical pan-genome analysis with suffix skips
With the rise of improved sequencing technologies, genomics is expanding from a single reference per species paradigm into a more comprehensive pan-genome approach with multiple individuals represented and analyzed together. Here we introduce a novel O(n log n) time and space algorithm called splitMEM, that directly constructs the compressed de Bruijn graph for a pan-genome of total length n. To achieve this time complexity, we augment the suffix tree with suffix skips, a new construct that allows us to traverse several suffix links in constant time, and use them to efficiently decompose maximal exact matches (MEMs) during a suffix tree traversal. -
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Biogranat (Molecular Biology Graph Visualisation and Analysis Tool) is a new tool for the analysis and visualisation of large datasets.
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HRDAG
Framework for Hierarchical Graph Decomposition
This is a framework used to decompose hierarchical graphs, i.e.,graphs which were created from or contain a hierarchy of modules. Each module is reused several times in the hierarchy. This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets. -
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xPyder PyMOL Plugin
Analyze and visualize coupled residues and their networks in proteins
xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level. -
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nail_systems_biology
NAIL is a toolset for network analysis in the life sciences
The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results. These methods are designed as self-contained platform-independent components which can be called either from another program, or from a command line. Modelling biological systems as networks (graphs) is becoming a common approach in the life sciences. ... -
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CIG-P
CIG-P is a simple yet flexible data visualization tool
...CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. Publication: CIG-P: Cicular Interaction Graph for Proteomics http://www.biomedcentral.com/1471-2105/15/344/ Previously known as PIVOT (Protein Interaction Visualization and Observation Tool) -
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MolSig
The Stereo Signature Molecular Descriptor
An algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure, based on our previously introduced signature molecular descriptor. The algorithm can generate two types of descriptors, one which is compliant with the Cahn-Ingold-Prelog priority rules, and a faster one based on our previous definition of a directed acyclic graph that isaugmented to a chiral molecular graph. -
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GOFG Sports Computer
Free GPS tracking software for your workouts.
...The most important features are: - GPS tracking of your training - upload workouts to gofg.at and share them using twitter and facebook - analyze your exercises using a map-display & altitude graph - keep track of various statistics like ODO-meter - ships with English, German, Italian and Spanish user interface - export to Fitlog, TCX and GPX Currently Android, iOS and Windows Phone 7 & 8 are supported. -
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Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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ResCalc3
Spectral resolution calculator for MassLynx
...The resolution can be optionally compared to a threshold you specify and the result is displayed as Pass/Fail using a tick or cross alongside the resolution. You can choose to display a graph which shows the position and threshold result overlaid on the data. The resolution result can be printed and or copied into the clipboard so you can paste it into a report of your own. -
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FastAlign.pl
FastAlign is a perl script which uses the heuristic method of tfasty
...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 system - tfasty - Emboss (if you want a graphic) -
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Mix
Mix is a tool to combine multiple assemblies from NGS data.
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length. Please note that Mix has moved to: https://github.com/massyah/MIX -
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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
