Search Results for "seq" - Page 5
Sort By:
Showing 165 open source projects for "seq"
View related business solutions-
Our Free Plans just got better! | Auth0 by OktaYou asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your secuirty. Auth0 now, thank yourself later.
-
Bright Data - All in One Platform for Proxies and Web ScrapingBright Data offers the highest quality proxies with automated session management, IP rotation, and advanced web unlocking technology. Enjoy reliable, fast performance with easy integration, a user-friendly dashboard, and enterprise-grade scaling. Powered by ethically-sourced residential IPs for seamless web scraping.
-
1
This page contains the necessary software to characterize mappability of RNA-Seq reads and create a "blacklist" of genomic positions of mismapped reads. This blacklist can be used to filter potential false positives from variant or RNA editing calls. This software is described in "BlackOPs: Increasing Confidence in Variant Detection through Mappability Filtering" by CR Cabanski et al. Please cite this article if you use our software or available blacklists in your own analysis.
-
2
COV2HTML
A visualization and analysis tool of Bacterial NGS data for Biologists
... mapping coverage data (DNA-seq, RNA-seq, ChIP-seq and TSS) performed in different prokaryotic organisms (bacteria, viruses...) or different experimental conditions (mutant versus wild type strains or different growth states…) facilitating studies. -
3
rseqflow
RNA-Seq analysis pipeline for QC, Expression, DifferentialExpression
RseqFlow is an RNA-Seq analysis pipeline which offers an express implementation of analysis steps for RNA sequencing datasets. It can perform pre and post mapping quality control (QC) for sequencing data, calculate expression levels for uniquely mapped reads, identify differentially expressed genes, and convert file formats for ease of visualization. A detailed description of the pipeline] is given here: https://sourceforge.net/p/rseqflow/wiki/PipelineDescription RseqFlow offers two run mode... -
4
Protospacer
Rapid gRNA design and validation for CRISPR
... by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate. From here, users are able to evaluate potential off targeting, to export results in FASTA format or tabulated (e.g. for Microsoft Excel), and to connect to the Integrative Genomics Viewer (IGVref) and view target-sites in the context of genomic annotations, amino acid translations, and HT-Seq data (for off-target validation). We provide online video tutorials and a toy database from our main website. -
Build Securely on Azure with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
-
5
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. -
6
IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
-
7
pvaas
Program to identify Variants Associated with Aberrant Splicing
Alternative splicing is a precisely regulated process that involves interactions between cis- and trans-acting regulatory elements, and factors that disrupt these interactions can result in aberrant splicing. About 15-60% of human disease-causing mutations affect mRNA splicing rather than directly affecting coding sequences (López-Bigas, et al 2005, Krawczak M, et al, 1992). Deep transcriptome sequencing (RNA-seq) provides ability to interrogate both aberrant splicings and mutations... -
8
Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
9
BRACIL
ChIP-seq analysis tool
Binding Resolution Amplifier and Cooperative Interaction Locator (BRACIL) is a blind-deconvolution model that integrates ChIP-seq coverage with motif discovery. BRACIL predicts binding site locations with high-resolution and also cooperative interactions in ChIP-seq data. -
Build Securely on AWS with Proven FrameworksMoving to the cloud brings new challenges. How can you manage a larger attack surface while ensuring great network performance? Turn to Fortinet’s Tested Reference Architectures, blueprints for designing and securing cloud environments built by cybersecurity experts. Learn more and explore use cases in this white paper.
-
10
MendelChecker
QC for variant discovery from next gen sequence in pedigrees
MendelChecker is a likelihood-based measure of Mendelian segregation of Single Nucleotide Polymorphisms (SNPs) in nuclear pedigrees. We developed this method as a quality control measure for novel variant discovery from noisy next-generation sequencing data in pedigrees, such as Restriction site-associated DNA Sequencing (RAD-seq) in non-model organisms. This method implements comparison of heterogametic vs. homogametic transmission, i.e., sex linked vs. autosomal segregation. -
11
DeSQ
Seq: Gestore di processi sequenziali con esecuzione da smartphone
Progetto del corso di Ingegneria del software, Università degli Studi di Padova aa 2013/14 Gruppo DeSQ -
12
GIIRA
RNA-Seq driven gene finding incorporating ambiguous reads
GIIRA is a gene prediction method that identifies potential coding regions exclusively based on the mapping of reads from an RNA-Seq experiment. It was foremost designed for prokaryotic gene prediction and is able to resolve genes within the expressed region of an operon. However, it is also applicable to eukaryotes and predicts exon intron structures as well as alternative isoforms. -
13
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. -
14
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... -
15
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... -
16
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... -
17
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. -
18
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... -
19
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.
-
20
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... -
21
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. -
22
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.
-
23
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. -
24
GenomeRunner
Annotation and enrichment of Next-Gen sequencing data
Note: This version requires additional SQLite database files. Contact the developers to obtain them. Use http://www.integrativegenomics.org/ for the latest data and analyses. GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser. Input - any genome-wide data data in .bed format... -
25
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.