Search Results for "bam-readcount" - Page 3
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Showing 68 open source projects for "bam-readcount"
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TimeSheet
TimeSheet is a simple software for management activities
TimeSheet is a simple software for management activities. This software structure projects work orders (= clients) and activities (eg design, development, etc.) and allows you to track time to work on. -
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
.../MOUSE -format BED -pe TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -isize 200 -r 100 -pec (if control is PE) -ann -wig -seq –interfiles note: 1. Default species is HUMAN. Also supports MOUSE. Can add any other genome if in need. 2. Default format is BED. Also support ELAND. Will add SAM and BAM. 3. –r specifies read length (this is import through my experience). 4. –pe indicates pair-ended data. 5. If data is pair-ended, -isize refers to insert size (total length of a pair). -
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DeNovoCheck
DeNovoCheck: Inheritance analysis for NGS trio data
DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants. -
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cnvHiTSeq
cnvHiTSeq is a set of tools for detecting CNVs using sequencing data.
cnvHiTSeq is a set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. cnvHiTSeq uses standard BAM files as input. -
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samscope
A lightweight OpenGL SAM/BAM viewer
A lightweight OpenGL based interactive SAM/BAM viewer. Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. -
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ArchTEx
Accurate Extraction and Visualization of Next-Generation Sequence data
Quick extraction and visualization of NGS Data. Allows for calculation of strand cross-correlation to identify optimal short-read tag extension. Allows for extraction of data using a variety of data transformations. Performs genome-genome correlation of BAM files to assist in comparison of biological and technical replicates. http://bioinformatics.oxfordjournals.org/content/early/2012/02/02/bioinformatics.bts063.abstract -
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Altrans
Quantification of Splicing Events
Altrans is a method for the relative quantification of splicing events. It requires a BAM alignment file from an RNA-seq experiment and an annotation file in GTF format detailing the location of the exons in the genome. It uses paired end reads where one mate maps to one exon and the other mate to a different exon and/or split reads spanning exon exon junctions to count “links” between two exons. When there are overlapping exons, these are grouped into “exon groups” and unique portions of each... -
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MultiBamView was developed on BamView for displaying multiple Bam files simultaneously. It is useful in comparing several runs mapped to the same reference sequence, finding shared or unique mutations.
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This program minimizes boolean expressions. After combining minterms as far as possible, the program draws a chart of prime implicants which the user can easily read and manipulate to remove any remaining superfluous implicants.
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OpenBAM is a Business Activity Monitoring(BAM) application for Operations Managers in service organizations who are constantly trying to figure out what's effecting their business by trying to co-relate data from multiple systems.
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A really simple PHP program for indexing your gay porn (or whatever). The idea is that you just throw this script in your image directory and BAM -> thumbnails of stuff. Requires ImageMagick and 10-20 pictures of Gary Coleman.
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d64-web is web-enabled utility for displaying Commodore 64 (D64/D71/D81) disk image contents (directory, BAM and more). It also provides a basic API for working with D64 disk images in PHP. Up to this moment only works fully on D64 images.
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The Free BAM project provides a J2EE-based multi-channel Business Activity Monitoring (BAM), Notification and Interaction system and a set of tools to help IT organizations, consultants and developers deliver robust BAM-based solutions.
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motif_counter
Program to pull out specific motifs from bam sequence files
Motif counter is a simple bash script that allows users to scan all reads contained in a bam file for a specific motif sequence repeated a number of times. Designed to look for the number of variant telomere repeats and reads in a whole genome sequencing dataset. The program prompts for a character string, and the number of times that string should be present in each read, then pulls out the data. Motifs can either be consecutive or uncoupled from each other across the read, and analysis... -
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malty_DEPRECATED
translates alignments of A-to-B and B-to-C to A-to-C; has BAM support
Development moved to: https://bitbucket.org/rongchenlab/malty Docs moved to: http://malty.readthedocs.org/en/latest/