Search Results for "seq" - Page 7
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Showing 224 open source projects for "seq"
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Pro-Gyan
A user-friendly system to build and share classifiers from protein seq
This is to provide the executables and protein classifiers/model. The source code and documentations are available at https://code.google.com/p/pro-gyan/. -
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CHANCE-HT
ChIP-seq data pre-processing software
CHANCE-HT is a ChIP-seq pre-processing software that filters samples with weak IP-strength, identifies heavily biased control experiments and under sequenced samples, detects batch effects, and normalizes large ensembles of ChIP-seq datasets. CHANCE-HT uses a parallel processing approach to normalize and filter large collections of ChIP-seq datasets in tandem. -
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Bycom
Bycom can do methylcytosine calling (5mC calling) from BS-seq.
Bycom can do methylcytosine calling from BS-seq (WGBS and RRBS), and either unmapped reads (FASTQ) or mapped reads (SAM/BAM) could be permitted for the input data. Certain SNPs (C>A/G) can also be selected in the output. 1. There's no softwares or methods identify methylcytosines considering the cell heterozygosis caused by multicellular sequencing. Bycom introduced it along with the sequencing errors and unconverson rate based on the Bayesian model. 2. Several parameters in Bycom could... -
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snpSniffer
snpSniffer is a sample integrity checking tool for NGS data
-- About snpSniffer -- snpSniffer is a genotype based sample integrity checking tool for next generation sequencing data. It ensures no sample mixups have occurred by checking genotype concordance of carefully curated genomic loci. It currently works on whole genome, exome and RNA-Seq data. Identifying mixups involves 3 steps 1. Generate the genotypes in a vcf format at specific genomic loci 2. Adding the genotypes generated to a flat file "database.ini" provided 3. Compare... -
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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... -
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DNase2Hotspots
This software identifies tag-enriched regions(hotspots) from DNase-seq
DNase2Hotspots is a software package for identifying tag-enriched genomic regions (hotspots) from the DNase-Seq genomic data. This program reads a BAM (Binary Alignment/Map) file or tab-delimited text files as input and produces a list of hotspot candidates and associated z-scores as output. Mappability profiles for the reference genome and genomic regions of repeat maskers are also required as input. -
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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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AS-peak
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus identification of RNA-protein binding sites from high throughput sequencing data presents unique challenges. While peak identification in CHIP-Seq data has been extensively explored, there are few bioinformatics tools tailored to peak calling on the analogous datasets for RNA-binding proteins. Here we describe ASPeak, an implementation of an algorithm that we previously applied to detect peaks in Exon Junction Complex... -
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BriPy
A BRIC-seq data analysis package written in Python.
-What is BRIC-seq? BRIC-seq, short for 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis, is a novel method in Next Generation Sequencing (NGS) to determine the RNA stability of each transcript. It employs metabolic labeling by BrU of newly synthesized RNAs to chase chronological decreases of BrU-labeled RNA (Pulse-chase labeling), followed by immunoprecipitation with antibody for BrU, construction of cRNA library for High-throughput sequencing and computational data... -
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Pop-seq
Population simulator to solve next generation sequencing questions
Pop-seq is a perl based simulation tool, for generating any kind of mapping population using an user defined recombination landscapes. Combined with the Seq-sim tool you can generate pooled or bar-coded next generation sequencing biased outcomes. This tool were used to solve reappearing question in a experimental design (e. g. of how many plants or sequencing depth is advisable in a back crossed or out crossed scenario ) -
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FOCIS
FOCIS finds features for functional follow-up
FOCIS (Feature Overlapper for Chromosomal Interval Subsets) performs an interval-based screen of a database of genomic features – ChIP-seq peaks, motif matches, and others – for overlap enrichment at a specific subset of genomic regions relative to a dataset-matched background. It was recently used to discover a novel enhancer that mediates drug resistance in melanoma. -
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RNA-Seq-Simulator
Realistic simulation of RNA-Seq short reads
A suite of Python programs to produce simulated Illumina RNA-Seq reads with a high level of realism. The starting positions of the reads and the distributions of read errors and quality codes are all empirically derived from real RNA-Seq datasets. The suite includes Python scripts to prepare the empirical read creation probability and read error distribution tables, and to generate and postprocess the simulated reads. -
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method. It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs... -
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PennCNV-2 is the second major release of the popular program PennCNV, which was originally designed for inferring copy number variation in germline DNA using data from genotyping microarrays. PennCNV-2 now supports inference of copy number abberrations in tumor cells (PennCNV-tumor). New functionality for inference of copy number variation using next gen sequencing data is under development (PennCNV-Seq). The software is written in C++ and targeted for unix/linux platforms.
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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide. It can be easily adapted for other genomes.
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Software de análise e seq genético
Identifica anomalias no genoma humano.
Identifica anomalias no genoma humano, como troca de nucleotídeos comparando sequencias de pacientes e sequencias de referencia e controle. -
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GENE-counter is a computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression of eukaryotes, prokaryotes, as well as organisms with no available genome reference sequence.
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Dress Up RNA seq
End-to-end automated pipeline of RNA seq packages for an HPC system
The purpose of DressUp is to create an end-to-end RNA seq pipeline in which all of the steps of analyzing data from an Illumina sequencer is done in one step in an HPC environment. RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs... -
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TFAST
Software for analysis of afSELEX-seq data
Transcription Factor Analysis using SELEX with High-Throughput Sequencing (TFAST) is software developed by the Mobley lab at the University of Michigan designed to assist with transcription factor binding site discovery using data generated from aptamer-free SELEX-seq (afSELEX-seq). -
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Tuque
Tools for mapping RNA-Seq reads to eukaryotic genomes
Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals -
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Webapp
A web interface to the SnowyOwl gene prediction pipeline
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rTRM
Identification of transcriptional regulatory modules (TRMs)
This R package can be used to identify TRMs using experimental evidence from a single ChIP-seq experiment. It combines computational predicted transcription factor (TF) binding sites, gene expression and protein-protein interaction (PPI) data and use it to predict TRMs. -
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Arpeggio
Harmonic analysis of ChIP-seq experiments
Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated datasets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment to large repositories of publicly available profiles. Arpeggio allows us to efficiently compare numerous ChIP-seq datasets consisting of many types of DNA-binding proteins collected from a variety... -
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rnasimulase
Simulation of allele-specific RNA-seq data
Simulation of allele-specific RNA-seq data