Search Results for "genome wide mapping"
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Showing 155 open source projects for "genome wide mapping"
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Matplotlib
matplotlib: plotting with Python
..., ...), and a projection and mapping toolkit (Cartopy). Matplotlib is the brainchild of John Hunter (1968-2012), who, along with its many contributors, have put an immeasurable amount of time and effort into producing a piece of software utilized by thousands of scientists worldwide. Matplotlib is a Sponsored Project of NumFOCUS, a 501(c)(3) nonprofit charity in the United States. Matplotlib has support for visualizing information with a wide array of colors and colormaps. -
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Traccar
Traccar GPS Tracking System
The Traccar software offers exceptional performance and stability, whether it is installed on Windows, Linux, or any other platform. The server can be hosted on-premise or in the cloud, and we provide various hosted options with professional support. Traccar stands out among GPS tracking systems on the market by supporting a vast array of protocols and device models. Whether you prefer low-cost, no-name GPS trackers or high-end, quality brands, Traccar enables you to choose from a wide... -
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Boltons
250+ constructs, recipes, and snippets which extend the Python library
Boltons is a set of pure-Python utilities in the same spirit as, and yet conspicuously missing from, the standard library. Due to the nature of utilities, application developers might want to consider other integration options. Boltons is tested against Python 2.6-2.7, 3.4-3.7, and PyPy. The majority of boltons strive to be “good enough” for a wide range of basic uses, leaving advanced use cases to Python’s myriad specialized 3rd-party libraries. In many cases the respective boltons module... -
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Mudlet
Cross-platform, open source, and super fast MUD client with scripting
Play immersive, multiplayer, pure-text games on Mudlet. Performance defined Mudlet from its birth. The custom text display and the Lua-powered scripting system will handle the biggest raids without issues. Mudlet’s entire user interface is designed to be modded – from the space within the window to the look and feel of the client itself. Make yourself a beautiful portal to your text world. Mudlet is completely free to download, modify, and extend. Build on top of a powerful foundation and... -
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The SpeechBrain Toolkit
A PyTorch-based Speech Toolkit
... in a wide variety of realistic applications. SpeechBrain provides different models for speaker recognition, including X-vector, ECAPA-TDNN, PLDA, and contrastive learning. Spectral masking, spectral mapping, and time-domain enhancement are different methods already available within SpeechBrain. Separation methods such as Conv-TasNet, DualPath RNN, and SepFormer are implemented as well. SpeechBrain provides efficient and GPU-friendly speech augmentation pipelines and acoustic features extraction. -
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Oat++
Light and powerful C++ web framework for web applications
Oat++ has zero dependencies and it's easily portable with a wide range of supported platforms. With Oat++ Simple-API it's easy and fun to build flexible and robust APIs. With Oat++ Async-API you can handle over 5 Million concurrent connections on a single server. Oat++ ORM provides an easy and unified way to access databases. Oat++ relies on Object-Mapping throughout its codebase to ensure consistency of APIs and data models. Automatically document endpoints with Swagger-UI and OpenAPI 3.0.0... -
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INI
Package ini provides INI file read and write functionality in Go
The most powerful, convenient and popular Go package for INI manipulations existed on Earth. Not limited to reading from a file, parse from []byte type raw data, or streaming from io.ReadCloser works like a charm. Wide-range support of variant formats includes but is not limited to my.cnf, .gitconfig, or even unparseable sections. Automatically convert to native types of Go at no cost. Let you focus on the code logic and no more tedious conversions. Map your configuration to a user-defined... -
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OSGeoLive
Bootable linux distro for Geospatial Applications
OSGeoLive is a self-contained bootable DVD, USB thumb drive or Virtual Machine based on Lubuntu that allows you to try a wide variety of open source geospatial software without installing anything. It is composed entirely of free software, allowing it to be freely distributed, duplicated and passed around. It provides pre-configured applications for a range of geospatial use cases, including storage, publishing, viewing, analysis and manipulation of data. It also contains sample datasets... -
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A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data.
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Lep-MAP3 is a novel and free software for linkage mapping. It can construct linkage maps on very large number of markers and individuals on single or multiple families. Especially, it supports whole genome sequencing data even with low sequencing depth. If you use Lep-MAP3, please cite P. Rastas. Lep-MAP3: Robust linkage mapping even for low-coverage whole genome sequencing data, Bioinformatics. 2017, 33(23):3726-3732. https://doi.org/10.1093/bioinformatics/btx494. Please note Lep-Anchor...
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popoolation
estimate natural variation and positive selection
PoPoolation is a pipeline for analysing pooled next generation sequencing data. Currently PoPoolation allows to calculate Tajima’s Pi, Watterson’s Theta and Tajima’s D with a sliding window approach for chromosomes or for set of genes. One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. We believe that PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. Documentation: https... -
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering... -
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miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
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MensorGIS
Open Source Desktop GIS with Surveying and Cartography Functionality
Open Source Desktop GIS with Surveying and Cartography Functionality. Should be seen as a Learn-GIS with basic Algorithms and Functionality in VB.NET and C#.NET without usage of Software Libraries: CAD/GIS Data (DXF, ShapeFile, GML2, GPX, KML, CSV), Data Schema, Query, Analysis, Topology, Contours, Ortho-Image Registration, Least Squares Adjustment. Also world-wide Geodata of Countries and POIs are available. A companion Scriptum gives explanation about the Theory behind MensorGIS. -
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PuntoGPS
Minimalistic wide-open GPS-locator/tracker
PuntoGPS is a simple tracking application to show your position to others, e.g. during urban bike rides :) It's made up of a GPS tracking app and a web based map. The app can be run on any GPS equipped device (smartphone, tablet, etc) by the users that want to show their position and/or track their paths. No user account is required, but users can set a short status message to identify (the default is the device name). The web map shows the current position of the active users,... -
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FLO (Markup Language)
FLO: a simple markup language to write flowcharts with any text editor
FLO is a simple markup language to write flowcharts with any text editor. FLO is a free and open-source plain text markup language that makes it possible to write a flowchart in any text editor, using a simple, easy-to-understand and readable text format. With its simple text format, FLO allows users to easily create diagrams and visual representations of even the most intricate concepts. Whether you are an engineer, scientist, educator, storyteller, or just someone who wants to... -
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treeminder
a free mind mapping tool, to especially assist decision making
I've been trying to develop an idea of a project, but the wide range of possibilities with all their outcomes, cons and pros and whatnot got my mind overloaded. There was no way I could keep or process that much information with my bare mind. So, I've checked the mind mapping tools available in the market, both free and commercial ones, yet they were either clunky or overkilling for my needs. Thus, I've made my own thing, and decided to share it with everyone who might find it useful... -
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PhaseDel
Phasing-based somatic deletion caller from single-cell WGS data
... heterozygous SNP sites. The important features of PhaseDel are: • Accurate identification of somatic focal deletions at single-base-pair resolution in scWGS using phasing information • Estimation of the genome-wide somatic deletion rate for a given cell with the controlled FDR level • Characterization of underlying DSB repair mechanisms for identified deletion candidates A more detailed description of the tool is provided in the [[wiki]] tab. -
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MAGeCK
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support from... -
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YeastpRofileSpearman
Software to calculate profiles around TSS and TTS of yeast mRNAs
YeastpRofileSpearman is a portable Windows form application, written in C#, to compute the profile of a genomic variable around transcription start (TSS) and termination (TTS) sites of yeast mRNAs. It is variation of the software application YeastpRofile (https://sourceforge.net/projects/yeastprofile/) in which Spearman’s rank correlation coefficient (Rs) is computed in place of Pearson correlation coefficient. The profile is obtained by calculating the genome-wide Rs between the genomic... -
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GenoCline
GenoCline is a free Java software for genetic cline analysis
Identification of clines from allele frequency or genome-wide databases. Angular transformation. Sigmoid function. Parameterization of a cline: orientation, Pearson’s product-moment correlation coefficient, linear and sigmoid regression and coefficient of determination. Graphical representation of the cline. Confidence limits. Spatial autocorrelation. Moran's index. Isolation by distance. Exponential regression. Correlation Fst/Distance. Centroid method. Cline's expected vs. predicted... -
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mimicree2
Genome-wide forward simulations of evolving populations
MimicrEE2: genome-wide forward simulations of adapting populations. For a detailed description, a manual, several walkthroughs and the validation see https://sourceforge.net/p/mimicree2/wiki/Home/ -
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GMATA software for Genomic SSR marker
Genome-wide Microsatellite Analyzing Toward Application: GMATA
What is software GMATA v21 Genome-wide Microsatellite Analyzing Toward Application (GMATA) is a software for Simple Sequence Repeats (SSR) analyses, and SSR marker designing and mapping in any DNA sequences. It has the following functions: 1. SSR mining; 2. Statistical analysis and plotting; 3. SSR loci graphic viewing; 4. Marker designing; 5. Electronic mapping and marker transferability investigation. GMATA is accurate, sensitive and fast. It was designed to process large genomic... -
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gradslam
gradslam is an open source differentiable dense SLAM library
gradslam is an open-source framework providing differentiable building blocks for simultaneous localization and mapping (SLAM) systems. We enable the usage of dense SLAM subsystems from the comfort of PyTorch. The question of “representation” is central in the context of dense simultaneous localization and mapping (SLAM). Newer learning-based approaches have the potential to leverage data or task performance to directly inform the choice of representation. However, learning representations... -
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LDhelmet
Fine-scale recombination rate estimation.
NOTE: This project has migrated to GitHub: https://github.com/popgenmethods/LDhelmet LDhelmet performs statistical inference for fine-scale variable recombination rate estimation. The source code and the recombination maps for two populations of Drosophila melanogaster are available for download. Reference: Andrew H. Chan, Paul A. Jenkins, Yun S. Song (2012). Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster. PLoS Genet 8(12): e1003090. doi:10.1371...