Search Results for "seq" - Page 8
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Showing 256 open source projects for "seq"
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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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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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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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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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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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ChipSeqAnalyzer is a python program aimed at discovering transcription factor binding sites, originally in the yeast Candida glabrata. It takes Chip-Seq data as input, and outputs html reports from RSAT / Peak-motifs.
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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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Tag-find
a python script to recognize specific sequence of tags
Tag-find is a python script developed to clean up reads from a specific 12 nucleotides long tag sequence used during the cDNA library preparation for RNA-seq experiments. -
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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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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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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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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... -
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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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FindPrimersInReads
Finds "primers" in fasta files, e.g. RNA-Seq data
These tools allow for searching large data sets for short "primer" sequences, allowing for a configurable number of mismatches. -
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qure
software for viral quasispecies reconstruction from next-gen seq. data
QuRe is a program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) NGS data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral... -
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rnasimulase
Simulation of allele-specific RNA-seq data
Simulation of allele-specific RNA-seq data