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Showing 27 open source projects for "read"
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In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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silico
Libraries and scripts for molecular modelling written in Perl
A perl molecular toolkit designed to assist in general molecular modelling activities. Silico provides file format conversion, molecular manipulation and analysis and a simple way to write wrapper scripts around other preexisting software packages. -
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SDF or Structures Data File is a file format developed by MDL to handle a list of molecular structures with associated properties. The SDF toolkit provides small tools to read and parse SDFs, filter, and add/remove properties.
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guglinatts-en
Guglina TTS, special edition: in English (guglinatts-en)
Guglina TTS, special edition: in English (guglinatts-en), is a voice synthesizer originally designed for Brazilian Portuguese. Uses the Google Translate text-to-speech API. Read screens for the visually impaired. Transforms text into audio, allowing blind or low-vision people to access content displayed on the screen. Although the main target audience for text-to-speech conversion systems - such as Guglina TTS EN - is people with visual impairment, this type of program can be used by people with dyslexia and other reading disabilities, people with severe as well as by pre-literate children. ... -
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bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files for visualization, and (9) support for advanced sequencing technologies such as TAB-seq, OxBS-seq, MAP-it, and NOMe-seq. -
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owfs and owhttpd
Project moved to https://github.com/owfs/owfs/
...Basically you can use these inexpensive little sensors and other chips with very simple wiring to sense and control the physical environment. The interface is very flexible -- everything from a web browser, to read and writing directly to the chip's "file" to integrating with your programs -- even over the internet. There is a growing number of 1-wire sensors: temperature, voltage, humidity, light, ultraviolet, pressure, thermisters, thermocouples, programmable microcontrollers, relays, lights, LCD panels, etc -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
...https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. Source code with user manual and installation guide of VFS is available at sourceforge's "Files" section. ... -
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MITP
MITP - conserve & novel miRNA identification & target prediction tool
...You also can run step by step using each step program. Please run these step programs at the same directory for running main program MITP.pl. Some steps are optional (read filter, expression, miRNA class and target). When you select the related parameters belong to these optional steps, the program will run these steps. Otherwise, it skip these steps. -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining. -
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Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
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TE-locate
a tool for calling transposons
TE-locate is a tool to locate all copies of sequences in a reference sequence using read-pairs. TE = Transposable Element Input is NGS-data. Please download all files first (including the demo data) and make your first run then. -
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IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
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...We now output JSON objects and I'm working on HBase integration. By outputting to JSON it also leaves open the possibility for on the fly in memory correlation between events. Read the included README before starting, it has a quick start guide and info on the constructors.
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slurp
IO buffering in parallel environments with large files
'slurp' and 'glurp' are related utilites that help with buffering of file input and output (IO) in parallel environments with large files. They read and write files using a much larger buffer than typical system and program defaults. -
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ForeRunner X01 toolkit provides an easy access to Forerunner 201/301/305/305E GPS-units. There are multiple command line tools to read data from GPS into database and tools to export data in different formats like gpx and tcx.
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the following paper: Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. ...
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Parallel Port Control Made Easy - parashell allows control of a PC parallel port (input and output) with simple command line arguments. The simplicity of these programs make it very easy to use in scripts. Control stepper motors, Relays, LEDs, etc...
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On December 8, 2009 the UK Met Office released records of worldwide land surface temperature readings. This project analyzes these records and produces output files that can be read by gnuplot and Google Earth to show temperature trends.
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A Perl script that interfaces with the Devantech USB to I2C interface adapter. This script allows a user to read and write as a master to the i2c bus as well as set or get the value of the io pins.
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A generic geospatial analysis and viewing capability using Perl scripts that provides the foundation and structure for readily creating KML data files from disparate data sources. KML files can be read and viewed by Google Earth and other tools.
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...Phenotype info for EBV-LCLs (HAPMAP CEU) for a minor histocompatibility antigen (mHag) specific T cell is input. Output is the region containing the mHag. A step-by-step read-me will be included.Email r.m.spaapen@umcutrecht.nl for help.
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UMD Overlapper takes a set of reads and quality data and determines which read pairs plausibly overlap; that is, it determines the pairs of reads containing subsequences that are similar enough that they may have come from overlapping parts of the genome.
