Search Results for "annotation"
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Showing 22 open source projects for "annotation"
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Praat
Doing Phonetics By Computer
Praat is a speech analysis application and source repository for doing phonetics by computer. It was created by Paul Boersma and David Weenink at the University of Amsterdam. The software lets researchers, linguists, clinicians, teachers, and students analyze, synthesize, manipulate, and annotate speech recordings. It supports acoustic inspection through waveforms, spectrograms, pitch tracks, formants, intensity, and related phonetic measurements. Praat also includes scripting tools for... -
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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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LPub3D
LDraw™ editor for LEGO® style digital building instructions.
LPub3D is an Open Source WYSIWYG editing application for creating LEGO® style digital building instructions. LPub3D is developed and maintained by Trevor SANDY. It uses the LDraw™ parts library, the most comprehensive library of digital Open Source LEGO® bricks available (www.ldraw.org/ ) and reads the LDraw LDR and MPD model file formats. LPub3D is available for free under the GNU Public License v3 and runs on Windows, Linux and macOS Operating Systems. LPub3D is also... -
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The Video Annotation and Reference System (VARS) is a software interface and database system that provides tools for describing, cataloging, retrieving, and viewing the visual, descriptive, and quantitative data associated with video.
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haikuVM
A Java VM for ARDUINO and other micros using the leJOS runtime.
HaikuVM has been started for hobbyists who develop applications for ARDUINO to open the world of JAVA and leJOS. Yes, you can program an ARDUINO with JAVA! HaikuVM is so small that it even runs on an atmega8 (and the ASURO robot). And yes, you can program an ASURO robot with JAVA! And since version 1.4.0 the RCX lego brick. -
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The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.
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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
...It can accept PWMs, such as those available in the Transfac or Jaspar databases as well as plain-text PWMs. It computes all occurrences of the PWM in the genome sequence for a given p-value threshold or cut-off. The match list is provided in various genome annotation formats, including BEDdetail, FPS, and SGA. -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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ParTools
Support for manual parallelization of sequential C programs.
ParTools allows the interactive analysis of a C program execution profile and data dependencies to facilitate the discovery and selection of suitable parallelization candidates in a manual parallelization process. The flow does not assume any specific parallelization technique, thus it can be broadly applied. The original (serial) C source is automatically annotated to trace the execution profile and data dependencies at run-time. The annotated program is then executed using a... -
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. ... -
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VCF Explorer
A desktop application for analyzing whole genome VCF files
...Efficient memory management of the program and the elimination of preliminary parsing step enable to carry out the analysis at ordinary computers. VCF-Explorer presents an easy to use environment where various types of queries for the annotation and the samples can be defined. VCF-Explorer can be run at different environments and computational platforms ranging from a standard laptop to an advanced server. -
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mwetoolkit
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/ The Multiword Expressions toolkit aids in the automatic identification and extraction of multiword units in running text. These include idioms (kick the bucket), noun compounds (cable car), phrasal verbs (take off, give up), etc. Even though it focuses on multiword expresisons, the framework is quite complete and can also be useful in any corpus-based study in computational linguistics. The mwetoolkit can be... -
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steam-sim
An accurate, scalable, and energy-aware simulator for WSNs
STEAM-Sim establishes a hardware/software/network co-simulation of wireless sensor networks. Original C code is used in simulation. The code is natively executed by the cpu where the simulation is run. The time annotation engine annotates the C source code used for simulation with the timing information as if the code is run on a microcontroller. The annotation process is fully automated. Hardware models are developed using the PAWiS framework and reflect the timing, functionality, and energy-consumption of real-world hardware such as a CC2420 radio transceiver. ... -
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HRSS
Hybrid Relative Specificity Similarity based on Gene Ontology
This software provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products. The software uses the pre-downloaded GO database files and the GO annotation files. It allows the users to set organisms, and evidence codes ignored. The software is composed of five modules, getGODAG, getGOAnno, hrssmatrix, hrsstps and hrsspps. -
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ParsEval is a program for comparing alternative sources of gene structure annotation (provided as GFF3 files) for a genomic sequence (or set of sequences). Similarity statistics are reported in a single aggregate summary report, as well as for each gene locus individually.
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Gromit-MPX is a multi-pointer GTK3 port of the original Gromit desktop annotation tool. It enables graphical annotations with several pointers at once and is A LOT faster than its predecessor since it uses the XCOMPOSITE extension where available.
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A library with a large (sparse) array mapping each unicode code point to the annotation data for it provided in http://www.unicode.org/Public/UNIDATA/NamesList.txt
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Celsius is a data warehouse that provides web services for upload, archival, download, annotation, quantification, and normalization of all Affymetrix microarray platforms.
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Kelp is a source code annotation framework. Written in strict ISO C90 with support for Posix and Windows environments. Large file support. Supports both 32 and 64 bit platforms. Plugins for Vim and Eclipse are available.
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Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.
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CANNOT - Coyote Annotation. This framework was developed in JAVA and its API's facilitates to the reuse of code and the sharing of information through to the architecture in layers and standard ISO MPEG-7 used for the Digital Video Content Annotations..
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Template database is a novel relational database that provides schema freedom. The current implementation is on top of PostgreSQL. It has interesting properties that make it suitable for data analysis / annotation / modeling.
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