Search Results for "annotation"
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Showing 184 open source projects for "annotation"
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The AI workplace management platformBy combining AI workflows, predictive intelligence, and automated insights, OfficeSpace gives leaders a complete view of how their spaces are used and how people work. Facilities, IT, HR, and Real Estate teams use OfficeSpace to optimize space utilization, enhance employee experience, and reduce portfolio costs with precision.
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Outbound sales softwareAdversus is an outbound dialing solution that helps you streamline your call strategies, automate manual processes, and provide valuable insights to improve your outbound workflows and efficiency.
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing customizable databases so researchers can bias domain or strain-specific annotations. ... -
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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Zotero PDF Translate
Translate PDF, EPub, webpage, metadata, annotations, notes
Zotero PDF Translate is a plugin for Zotero that enhances the research workflow by enabling in-app translation of PDFs, EPUBs, webpages, and associated metadata directly within the Zotero interface. It integrates seamlessly with Zotero’s document reader, allowing users to select text and instantly receive translations in a pop-up or side panel without leaving the application. The plugin supports a wide range of translation services, including both free and API-based providers, giving users... -
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Segments.ai
Segments.ai Python SDK
Multi-sensor labeling platform for robotics and autonomous vehicles. The platform for fast and accurate multi-sensor data annotation. Label in-house or with an external workforce. Intuitive labeling interfaces for images, videos, and 3D point clouds (lidar and RGBD). Obtain segmentation labels, vector labels, and more. Our labeling interfaces are set up to label fast and precise. Powerful ML assistance lets you label faster and reduce costs. Integrate data labeling into your existing ML pipelines and workflows using our simple yet powerful Python SDK. ... -
Get full visibility and control over your tasks and projects with Wrike.Wrike offers world-class features that empower cross-functional, distributed, or growing teams take their projects from the initial request stage all the way to tracking work progress and reporting results.
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astap program
Stacking program, astrometric (plate) solver, fits file viewer
... - Alignment using an internal star match routine, internal Plate Solver, manual or ephemeris. - FITS viewer with swipe functionality, deep sky and star annotation, photometry and CCD inspector. - Annotation of solar and deepsky objects. - Photometry of point sources, extended sources and variable stars - Blink routine for astro images. -
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MyBatis Mapper4
Mybatis common mapper, easy to use
This book starts with a simple MyBatis query to build a basic development environment for learning MyBatis. Through a comprehensive sample code and test, the basic usage of adding, deleting, modifying, and checking operations in the MyBatis XML mode and annotation mode is explained, and the application of dynamic SQL in different aspects and the best practice program in the use process are introduced. Provides a wealth of examples for MyBatis advanced mapping, stored procedures, and type processors. Through a bottom-up approach, readers can better understand and master the advanced usage of MyBatis. ... -
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PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/
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SPPAS
SPPAS - the automatic annotation and analyses of speech
SPPAS is a scientific computer software package written and maintained by Brigitte Bigi of the Laboratoire Parole et Langage, in Aix-en-Provence, France. Available for free, with open source code, there is simply no other package for linguists to simple use in the automatic annotations of speech, the analyses of any kind of annotated data and the conversion of annotated files. SPPAS is able to produce automatically speech annotations from a recorded speech sound and its orthographic... -
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Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.
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The full-stack observability platform that protects your dataLayer, tags and conversion dataCode-Cube.io detects issues instantly, alerts you in real time and helps you resolve them fast. No manual QA. No unreliable data. Just data you can trust and act on.
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
...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, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. A complete list of functionalities is available in our wiki (https://sourceforge.net/p/ngsep/wiki/Home/). ... -
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Tokenized Text Aligner
Aligns tokens in two versions of a text with differing tokenization.
...It is intended for use in the preparation of annotated linguistic corpora, where differences in tokenization may arise (i) following corrections or modifications to the source text or (ii) through the creation of different layers of annotation (part-of-speech, treebank) requiring different tokenization. In its default implementation, it produces a human-readable CSV table associating tokens in text A with tokens in text B, and can also inject token-level annotation from text B to text A. The Aligner class on which the default implementation is based can be incorporated into more complex workflows. -
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miRge3
Comprehensive analysis of small RNA sequencing data
An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). ... -
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LaBB-CAT
A linguistic annotation store
LABB-CAT is a browser-based linguistics research tool that stores recordings and regular-expression searchable text transcripts of interviews. The search results, entire transcripts, and media, can be viewed or exported in a variety of format -
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XLibraryDisplay
A sequence analysis tool for protein engineering
XLibraryDisplay is an intuitive sequence analysis program optimized for protein engineering. It is ideal for all directed evolution platforms including phage, ribosome, and yeast display. Analysis can be quickly done on hundreds to thousands of sequences. Best suited for Sanger sequencing. Requirements: Microsoft Windows XP, 7, 8, or 10 and Excel 2007, 2010, 2013, or 2016 Described in Stafford et al JCIM 2014: http://pubs.acs.org/doi/abs/10.1021/ci500362s -
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CpDB
Relational database schema and tools for bacterial genome annotation
This software allows us to create a relational database in PostgreSQL hosting full bacterial genomes. Besides the database, there is software, like a parser, to convert EMBL or GBK files to the CpDB relational schema. Once in the CpDB, one can extract unlimited reports from bacterial genomes using SQL. This software is part of the Ph.D. in Bioinformatics from Anderson Santos (https://orcid.org/0000-0003-3418-0823) developed under the Corynebacterium pseudotuberculosis (Cp) pangenome project.... -
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Strings Edit
String editing and formatting library for Ada
Strings edit is a library that provides I/O facilities for integers, floating-point numbers, Roman numerals, and strings. Both input and output subroutines support string pointers for consequent stream processing. The output can be aligned in a fixed size field with padding. Numeric input can be checked against expected values range to be either saturated or to raise an exception. For floating-point output either relative or absolute output precision can be specified. UTF-8 encoded strings... -
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Image16
Image viewer/editor specialized in astrophotography 16bits processing
Opens/saves TIF, FITS, PNG, XISF, PXM, RAW, JPG, XCF, PSD, WEBP. AsinH, Sqrt, Ln, Exp and Sqr stretching, HSL and RGB adjusting, Levels and Curves adjusting and Background Extraction for Color Balance, Flatness and Gradient Correction. Arithmetic between images. Resizing and croping. Color Balance based on background, selection or stars B-V (after platesolving). Debayering/Bayering. Inversion, mirroring, rotation, barrel/pincushion correction. RGB alignment/shifting. Erode, Dilate, ...... -
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NeedLR
Welcome to NeedLR, a scientific tool for pointcloud annotation.
Welcome to NeedLR, a specialized tool for Needle-like precision in Labeling and Rendering point cloud data. NeedLR offers an intuitive interface for detailed annotation and visualization of pointcloud data, perfect for academic research, ecological studies, and forestry management. The application leverages advanced algorithms to efficiently process and annotate large-scale point cloud data, ensuring high accuracy and ease of use. To use NeedLR: Download and unzip the file and run the .exe Visit this project's Github here: https://github.com/GunnerStone/NeedLR -
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kSNP
kSNP4 does SNP discovery and SNP annotation from whole genomes
...Finished and unfinished genomes can be analyzed together, and kSNP can automatically download Genbank files of the finished genomes and incorporate the information in those files into the SNP annotation. No programming skills are required to use kSNP4 Gardner, S.N. and Hall, B.G. 2013. . PLoS ONE, 8(12):e81760.doi:10.1371/journal.pone.0081760 Gardner, S.N., T. Slezak, and B.G. Hall. 2015 Bioinformatics 31: 2877-2878 doi: 10.1093/bioinformatics/btv271 -
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VectreViewer: A vector-based file viewer
A Windows-based viewer currently supporting CDR & 2D DXF files
This is a Windows-based wireframe viewer currently designed for CDR & 2D R12 DXF files. The DXF renderer supports arcs, circles, lines and polylines. Support for SVG files is coming shortly. Go here to check for updates: https://www.vvwr.net -
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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 from different other source files from the corresponding folder. ... -
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sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
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MITRE Annotation Toolkit
A toolkit for managing and manipulating text annotations
The MITRE Annotation Toolkit (MAT) is a suite of tools which can be used for automated and human tagging of annotations. Annotation is a process, used mostly by researchers in natural language processing, of enhancing documents with information about the various phrase types the documents contain. MAT supports both UI interaction and command-line interaction, and provides various levels of control over the overall annotation process. -
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misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee that all files are the version used in the analysis. Also, please be aware that these were very much developed with expediency in mind - that is, the process was expected to be performed in its final form once; little care was given to optimising runtime or chaining scripts together, and sometimes external resources are accessed manually.
