Search Results for "seq" - Page 9
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Showing 256 open source projects for "seq"
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MspJI-seq_pipeline1.0
an pipeline for MspJI-digesting sequencing in DNA methylation study
MspJI-seq_pipeline1.0 is pipeline for MspJI-digesting sequencing in DNA methylation study. Modification-dependent restriction endonuclease MspJI digestion coupled with next generation sequencing could estimate the methylation state of "CNNR" Cytosine location in the genome by mapping high throughput reads to the reference sequences. MspJI-seq_pipeline1.0 is designed to be a general-purpose mapping program to handle these special characteristics of MspJI-seq. Its alignment is based on the open... -
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HPeak
A HMM-based algorithm for defining enriched regions from ChIP-seq data
HPeak is a hidden Markov model-based approach that can accurately pinpoint regions to where significantly more sequence reads map. Testing on real data shows that these regions are indeed highly enriched by the right protein binding sites. Command (single-end): perl /compbio/software/HPeak3/HPeak.pl -sp HUMAN/MOUSE -format BED -t TREATMENT.inp -c CONTROL.inp -n OUTPUTPREFIX -fmin 100 -fmax 300 -r 36 -ann -wig -seq -interfiles Command (pair-end): perl /compbio/software/HPeak3/HPeak.pl -sp... -
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JAVA Program to Sequence Diagram Generator. This tool tries to help on analysing and understanding the behavior of the code when developping JAVA applications by generating the respective Sequence Diagram automatically at program execution.
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CLIIQ
Accurate Comparative Detection and Quantification of Expressed Isoform
CLIIQ is a computational method for simultaneous identification and quantification of expressed isoforms from multiple samples in a population. Given the RNA-seq mapping results and gene annotation, CLIIQ reports the list of expressed isoforms in the sample(s) by solving the ILP (Integer Linear Program) problems. Before the wiki page is back, please check http://www.sfu.ca/~yenyil/cliiq.html for instructions for installation and execution of CLIIQ. -
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SAMMate
RNA-Seq Transcriptome Assembly and Analysis
SAMMate is a GUI software tool for processing SAM files. The software allows users to accurately estimate gene expression and isoform expression scores using short reads to generate wiggle files for visualization in UCSC genome browser and an alignment statistics report. -
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
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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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Seurat
A sequence analysis tool for normal/tumor DNA and RNA data.
THIS IS NO LONGER THE HOME FOR SEURAT. PLEASE GO TO https://sites.google.com/site/seuratsomatic/ --- Seurat is an sequence analysis program for somatic mutation and allelic imbalance discovery in paired tumor and normal genome and transcriptome data. -
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GLMNB
GLMNB: a shape-based peak calling tool for ChIP-Seq data analysis
This is the beta-version of a shape-based peak calling tool for ChIP-Seq data analysis. It is built using Generalized Linear Model with Negative binomial distribution. This tool accounts for the common peak shape, local variability of peak shifting distance and negative binomial background noise. -
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R-SAP
RNA-Seq analysis pipeline
R-SAP is a user-friendly and fully automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets. R-SAP accurately characterizes various classes of transcripts resulted from aberrant splicing and chimeric transcripts. Expression level estimates are reported as RPKM (reads per kilobase of exon model per million mapped reads) values. -
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XSeq
XSeq, a new peak-calling program used Markov-modulated Poisson process
XSeq, a new peak-calling program used Markov-modulated Poisson processes (MMPP) for analysis ChIP-Seq data of transcription factors (TFs). XSeq applied model-based statistic and a decomposed reads density function to fasten structure information of raw data, and then to infer genomic ChIP-enriched regions. -
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R4ChIPSEQ
Random Read Reduction in R for ChIPSEQ data
Random Read Reduction in R for ChIP-SEQ data -
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FusionFinder
Tool to find gene fusions in RNA-Seq data
This software takes FASTQ data from RNA-Seq projects and interrogates it for the presence of gene fusions. -
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Bis-SNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
Bis-SNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels... -
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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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pastool
PAS-seq analysis
perform PAS-seq analysis -
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TopicModelsRNA
Topic models for biological data
Platform-independent implementation of hierarchical models (topic models) for application to biological (RNA-Seq) data. -
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RNAseqR
RNA-seq expression analysis tool
RNAseqR is designed for expression analysis of RNA-seq data, and is best suited for analysis of multiple, unreplicated libraries. It is a C++ coded program currently compiled for Linux systems. With GUI and command line interfaces, it can do log, PPM, and/or RPKM (if lengths provided) transformations, as well as, statistical analysis for differential expression, using the negative binomial cumulative distribution function (CDF) or the R test statistic introduced for EST analysis by Stekel... -
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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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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