Search Results for "transcript" - Page 2
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Showing 51 open source projects for "transcript"
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TransGeneScan
TransGeneScan is a gene finding tool for metatranscriptomic sequences
...TransGeneScan incorporates strand-speci c hidden states, representing coding sequences in sense and anti-sense strands on transcripts in a Hidden Markov Model similar to the one used in FragGeneScan (http://fraggenescan.sourceforge.net/), and can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. -
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MSProGene
Integrative proteogenomics beyond six-frames and SNPs
MSProGene constructs customized transcript databases for tandem mass spectra search. RNA-Seq data is used to generate transcripts and to resolve shared peptide protein inference in a proteogenomic network. -
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TranscriptDecoder
Extracting likely coding regions from transcript sequences
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PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
...guess-ft: Supervised search for fusion transcripts. guess-if: Supervised search for intragenic fusions. homology: Calculates homology between given two genes. frame: Predicts functional consequence of fusion transcript -
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Indiana Common Transcripts
Consume Common High School PESC XML transcript
Statewide initiative to produce code that will receive standardized PESC High School XML Transcripts, store them into an Oracle Database and then process the transcript into a university Student Information System -
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traph
A tool for transcript identification and quantification with RNA-Seq
Traph is a novel tool for transcript identification and quantification with RNA-Seq data, based on minimum-cost flows. Our method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model. -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi-supervised anomaly detection strategy based on logistic regression. Multiple mapping reads with a unique location after filtering are rescued and reallocated to the most reliable candidate location. ... -
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BriPy
A BRIC-seq data analysis package written in Python.
...It can calculate RNA half-life for each transcript and draw graphs describing the kinetics of RNA decay. In the future, it will provide several useful modules(e.g. calculating RPKM of each transcript from BAM file or ELAND output file). -Prerequisites To use BriPy package, you will need Python and the following extension packages. Python2.7 or higher NumPy SciPy Matplotlib -
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This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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EJCCMTools
Generation of EJCCM files from SAM/BAM files
EJCCMTools is a Java software package for compression of SAM or BAM files, performing subsequent gene or transcript expression profiling and visualizing gene read coverage profiles. This novel compression scheme reduces file size by a factor of 214 compared to BAM files while keeping the full ability to analyze and visualize gene and isoform expression levels. As a result of the compression EJCCM files are generated. These files can be indexed and queried using Tabix. -
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Transcription Aid
Transcription Aid helps you type text from recordings.
This software is to help type in text from speech recordings. It has several functions proven to help this type of work. However it is fully manual (aside from auto-completion), so no speech recognition if you are looking for that, but it is a great tool to do the job. -
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transqript
a program to transcript audio files
transqript can be used to transcribe audio files of interviews etc. to text files. -
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DETCT
Differential Expression Transcript Counting Technique pipeline
A perl pipeline for identifying differentially expressed genomic regions from transcript counting experiments. The pipeline first uses a Hidden Markov Model (HMM) to identify genomic regions based on the data from the experiment. During the sample counting step the pipeline removes reads which are suspected as being PCR duplicates. The differential expression analysis is currently performed using the DESeq package from Bioconductor. -
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Java library that implements the PESC College Transcript object and all dependent objects. It provides Marshalling and Unmarshalling from java objects to PESC XML files. To be used in an IDE such as eclipse for auto-completion of fields. The latest version (support for PESC CollegeTranscript 1.6) has been moved to github: https://github.com/jamhgit/pesc-transcript-jar
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The archive-crawler project is building Heritrix: a flexible, extensible, robust, and scalable web crawler capable of fetching, archiving, and analyzing the full diversity and breadth of internet-accesible content.
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GeneThello (read jə-ˈne-ˈthe-lō), is an acronym for genetic othello, an othello (reversi) playing program which based on Genetic Algorithm (GA). In principle GeneThello consist of an othello program and a genetic algorithm system.
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WebApp Go is an IDE for developing web applications easily with little to no effort. Follow us on Twitter now @WebAppGo. http:/;/twitter.com/WebAppGo
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A Sermon Content Management System based on asp.net. It allows for collection of: speaker, summary, topics, keywords, date, title and transcript information. Creates podcast of mp3 and allow for embedding of video from popular online video providers.
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Speech Made Visible is an experiment in showing some of the qualities of speech in printed text. Analyze a recording for attributes like pitch, intensity (loudness), and speed; then style the words in a transcript to suggest those characteristics.
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Until now the biggest chore for a DM was organizing his maps and notes in a way that they could be quickly found when needed. Now with this tool you can organize those notes and maps into a quick and easy to navigate HTML Document.
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A simple utility to help DMs track the combat of each encounter. It is designed to speed up the game play for the players by taking some of the calculation load off of the DM.
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Talks2 is a full Smalltalk and Development Environment which runs on top of the Java Virtual Machine. It comes with a ClassBrowser, Workspace, Transcript and all the things you know from a Smalltalk Development Environment.
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BlueBoy SIS is a full school admin program. You will be able to track a student from day one in your school. Enter grades for report card and transcript printing. Uses PHP4 and MySQL
