Search Results for "miarma-seq" - Page 9
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Showing 225 open source projects for "miarma-seq"
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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An analysis pipeline for mining exome-Seq and RNA-Seq data, focusing on quality control, SNP identification and annotation, RNA quantification, differentially expressed genes analysis, eqtl, and pathway analysis. http://seqgene.sourceforge.net
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We developed a RNA-Seq Data Annotation Pipeline named RNADAP, which measure genes expression in isoform level, work with high speed and less memory usage. Besides, our pipeline can be compatible with results from different mapping software.
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A peak caller for ChIP-Seq experiments that robustly handles short reads with *multiple* possible mappings. Releases are hosted here, but development source code is available at https://github.com/jakebiesinger/AREM. A Google group has been set up to help with questions from the community and for announcements of new builds. http://groups.google.com/group/arem-announcements
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DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.
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qips is a software package for analyzing ChIP-seq ("Chromatin ImmunoPrecipitation on sequencing") data. It finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.
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This is a set of programs to manipulate Commodore 64 Datasette tape files. These tools can convert a WAV file to a TAP file and vice versa, or extract PRG/SEQ files from a TAP file. Additional tools are planned to convert PRG/SEQ files to a TAP file.
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Kelp is a desktop genome visualization tool and API intended for custom and locally stored numeric, annotation and sequence data such as generated by high-throughput sequencing and genome-wide assays (microarray, LD, chIP-seq, etc). Linux/OSX/Win, C++/Qt
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SeqExpress is a cross-platform software that estimates gene/isoform expressioin level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.
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Batman-Seq: Basic Alignment Tool for MAny Nucleotides. A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.
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The Java class library, that contains classes for calculation of different mathematical relations between object and number sequences and sets: Kendall distance, Spearman distance, similarity measure, L1 distance and others.
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Download sequences files throw HTTP protocol, f.e. www.example.com/1.txt,...,www.example.com/10.txt. It works with XML configuration file and work with direct Internet connection and throw HTTP proxy.
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The Short Read Analysis Toolkit contains a number of useful tools to analyze data from ChIP-Seq and other experiments producing short sequence reads.
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Terminal based Midi Event Viewer (Alsa 0.9). It can autoconnect to alsa seq clients and provides simple filter mechanisms..
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A multi-platform sequencer that executes a sequence of events defined in XML. The sequence consists of action steps and flow control. The action XML tags are implemented as hooks calling plugins so they are user customizable.
