Serves as a transcriptome reconstruction method. Scripture is able to reconstruct a mammalian transcriptome with no prior knowledge of gene annotations. It exploits longer reads that span splice junctions to link discontiguous (spliced) segments. This software identifies short but strongly expressed transcripts, lower transcripts with aggregate evidence and precise gene structures for most of found lincRNA loci.
1 - 20 of 84
results
filter_list
Filters
1 - 20 of 84
results
Performs peak finding and downstream data analysis for next-generation sequencing analysis. HOMER affords several tools and methods to make use of ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and other types of functional genomics sequencing data sets. This software offers support to UCSC visualization, peaks annotation, quantification of transcripts and repeats or differential features, enrichment and expression.
Provides a range of functionalities for ChIP data analyses. CisGenome allows visualization, data normalization, peak detection, false discovery rate (FDR) computation, gene-peak association, and sequence and motif analysis. The software can handle data from two types of designs common in ChIP-seq experiments. The basic functionalities of CisGenome can be used in combination to address several different biological questions.
Allows analysis of ChIP-seq and other functional sequencing data. SPP is an R package providing a data processing pipeline optimized for detection of localized protein binding positions from unpaired sequence reads. This software can examine the saturation level of detected binding position to determine the amount of additional sequencing that may be necessary. It assesses also saturation properties and determines minimal saturated enrichment ratio (MSER).
Identifies peak regions in ChIP-Seq datasets that correspond to sites of transcription factor binding. PeakSeq scores the results of ChIP-Seq experiments by compensating for the mappability map and comparing against a normalized matching control dataset. This method was developed for use with tag sequence data from the Illumina Genome Analyzer platform. It can also be used to identify broader regions of binding that show significant enrichment relative to control.
Detects functional signals in tag profiles from different assays such as histone ChIP-seq, TF ChiP-seq, DNase-seq and FAIRE-seq. DFilter is based on a single receiver operating characteristic – area under the curve (ROC-AUC) optimizing algorithm. This software suits for genomic signals of individual cell types diluted in cellular mixture because the proportion of marginal signals can be mistaken for noise by suboptimal algorithms.
Analyzes data generated by short read sequencers. MACS is a standalone software dedicated to the forecasting of protein-DNA interaction sites from ChIP-Seq. The application is able to: (i) model the distance d and shifting tags by d/2 to enable the spatial resolution of the predicted sites; (ii) capture local biases in the genome by exploiting a dynamic λ local parameter and (iii) evaluate the false discovery rate (FDR) for each detected peak.
Serves for mapping and quantifying Mammalian transcriptomes by RNA-Seq. ERANGE includes features for performing different tasks: (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (‘multireads’), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, and (iv) compute the prevalence of transcripts from each known or newly proposed RNA.
A tool developed for DNase I hypersensitive sites (DHSs) identification. Popera identifies DHSs by applying the kernel density estimation algorithm. All the DHSs identified from various tissues and developmental stages were merged to create a unified DHS file; DHSs were then assigned unique ID tags. Normalized scores of unified DHSs were calculated for each unique tissue and developmental stage.
Provides a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations. QuEST offers the possibility to search de novo motif on ChIP-seq experiment and to perform gene ontology (GO) analysis on the ChIP-Seq data obtained from the NCBI Short Read Archive (SRA). This software is based on a realistic statistical modeling of the ChIP-Seq.
Enables comparative analysis of nucleosome physical organization at single-nucleotide resolution. DANPOS is a bioinformatics pipeline allowing dynamic analysis of nucleosome position and occupancy. The software is useful for detecting functionally relevant dynamic nucleosomes, not only in promoters in yeast, but also in distal regulatory regions with more fuzzy nucleosomes, in complex genomes such as those of mammalian.
Preprocesses HiChIP data. hichipper is a standalone application including functions for: (i) bias-corrected peak calling; (ii) library quality controlling (QC); (iii) DNA loop calling. The software generates files that can be exploited for downstream analysis and visualization as well as a QC report delivering information such as the efficiency of proximity ligation enabling the assessment of library preparation.
Recognizes ChIP-enriched regions in histone modification data. SCIER is based on a mathematical theory for the score distribution in a genomic background model of random reads. It finds spatial clusters, large and small, unlikely to appear by chance. This tool is able to deal with the enrichment context of a local window in determining its significance. It assists users to reduce the sampling fluctuations in the control library.
Creates a continuous tag sequence density estimation to identify biologically meaningful sites. F-Seq can summarize and display individual sequence data as an accurate and interpretable signal, allowing tag sequencing to identify specific sequence features like regions of open chromatin (DNase-seq) or transcription factor binding sites (ChIP-seq). Outputs results can be visualized through the UCSC Genome Browser.
Recognizes genomic regions enriched for sequenced reads across a wide spectrum of signal patterns and experimental conditions. ZINBA is based on a mixture regression approach that classifies genomic regions into three general components: background, enrichment, and an artificial zero count. It can preprocess data, determine significantly enriched regions, and refine boundary for more narrow sites.
A metaServer application designed for analyzing ChIP-seq data. It integrates several peak-finders within a single interface. A ChIP-seq data file can be analyzed using one or more of the peak-finders (up to 7 among MACS v1.3.7, CisGenome v2.0, Findpeaks v3.1.9.2, HPeak v1.1, E-range v.2.1, SeqSite v1.0 and SISSRs v1.4) and also produces consensus peaks.
A package for collating and searching across thousands of next-generation sequence (NGS) samples. Vancouver Short Read Analysis provides a database can be installed easily to rapidly access and store genetic variation information, compare data from any sequencing platform and perform aggregate analyses. The schema of the database makes rapid and insightful queries simple and enables easy annotation of novel or known genetic variations. Filtering can be done by utilizing annotations, matched pair datasets or datasets marked as non-cancer for separating polymorphisms from putative variants.
Allows users to conduct common analyses of RNAseq and ChIPseq data. SeqBox can be useful for genomic mapping, experimental power evaluation, differential expression, or transcription factors/histone-marks peaks identification, for instance. This tool is composed of SeqBox software and SeqBox target hardware.
A probabilistic method for jointly analyzing multiple ChIP-seq datasets. jMOSAiCS (joint model-based one- and two-sample analysis and inference for ChIP-seq) is a probabilistic model for integrating multiple ChIP-seq datasets to identify combinatorial patterns of enrichment. The key components of jMOSAiCS are base models for the sequencing reads of each individual ChIP-seq experiment and a model that governs the relationship of enrichment among different samples. It facilitates joint analysis of multiple ChIP-seq datasets for both identifying enrichment patterns of a single TF across multiple conditions and characterizing enrichment patterns of multiple epigenomic marks in one or more conditions.
A saturation-based ChIP-seq peak caller. Q uses an assessment of the quadratic enrichment of reads to center candidate peaks followed by statistical analysis of saturation of candidate peaks by 5' ends of reads. This method is not only substantially faster than several competing methods, but also demonstrates statistically significant advantages with respect to reproducibility of results and in its ability to identify peaks with reproducible binding site motifs.
0 - 0 of 0
results
1 - 20 of 26
results
filter_list
Filters
1 - 20 of 52
results
filter_list
Filters
1 - 20 of 52
results
HSV-1-induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes
Tools (3):
BEDTools, F-Seq, ChIPseeker
Topics (7):
ChIP-seq analysis, Human alphaherpesvirus 1, Canis lupus familiaris, Homo sapiens, Infection, Epstein-Barr Virus Infections, Herpesviridae Infections
P38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage
Tools (3):
Bowtie, MACS, DiffBind
Topics (1):
ChIP-seq analysis
Consequences of early life stress on genomic landscape of H3K4me3 in prefrontal cortex of adult mice
Tools (4):
Trimmomatic, Bowtie2, phantompeakqualtools, MACS
Topics (8):
ChIP-seq analysis, Mus musculus, Homo sapiens, Heredodegenerative Disorders, Nervous System, Movement Disorders, Brain Diseases, Demyelinating Autoimmune Diseases, CNS, Autoimmune Diseases of the Nervous System
Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins
Tools (5):
BWA, SAMtools, Picard, BEDTools, phantompeakqualtools
Topics (6):
ChIP-seq analysis, unidentified retrovirus, Homo sapiens, Caenorhabditis elegans, Physiological Effects of Drugs, Fatty Acids
Lsd1 regulates skeletal muscle regeneration and directs the fate of satellite cells
Tools (3):
Bowtie, HOMER, IGV
Topics (1):
DNase-seq analysis
SETDB1 prevents TET2-dependent activation of IAP retroelements in naïve embryonic stem cells
Tools (4):
Trim Galore!, Bowtie2, MACS, BEDTools
Topics (5):
DNase-seq analysis, ChIP-seq analysis, unidentified retrovirus, Mus musculus, Caenorhabditis elegans
Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation
Tools (3):
BCL2FASTQ Conversion Software, Bowtie, F-Seq
Topics (3):
ChIP-seq analysis, DNase-seq analysis, Mus musculus
Separase prevents genomic instability by controlling replication fork speed
Tools (3):
BCL2FASTQ Conversion Software, FastQC, MACS
Topics (3):
DNase-seq analysis, ChIP-seq analysis, Homo sapiens
The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia
Tools (3):
Bowtie2, MACS, BEDTools
Topics (4):
DNase-seq analysis, ChIP-seq analysis, Leukemia, Lymphoproliferative Disorders
BRG1-SWI/SNF-dependent regulation of the Wt1 transcriptional landscape mediates epicardial activity during heart development and disease
Tools (4):
Bowtie, MACS, BEDTools, ChIPseeker
Topics (11):
ChIP-seq analysis, Myocardial Ischemia, Urogenital Neoplasms, Urologic Diseases, Kidney Diseases, Neoplasms, Complex and Mixed, Wilms Tumor, Urologic Neoplasms, Neoplastic Syndromes, Hereditary, Metaplasia, Retinal Neovascularization
Identification of novel dysregulated key genes in Breast cancer through high throughput ChIP-Seq data analysis
Tools (3):
FastQC, Bowtie2, MACS
Topics (6):
DNase-seq analysis, ChIP-seq analysis, Homo sapiens, Breast Neoplasms, Breast Diseases, Neoplasms
Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering
Tools (6):
TopHat, DESeq2, Bowtie2, MACS, DiffBind, AmiGO
Topics (4):
Metatranscriptomic sequencing analysis, RNA-seq analysis, ChIP-seq analysis, Arabidopsis thaliana
YAP regulates cell mechanics by controlling focal adhesion assembly
Tools (4):
FastQC, Bowtie, HOMER, ChIPseek
Topics (2):
DNase-seq analysis, ChIP-seq analysis
Conserved roles for murine DUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons
Tools (4):
Trim Galore!, Bowtie2, MACS, MEME Suite
Topics (4):
DNase-seq analysis, ChIP-seq analysis, Mus musculus, Homo sapiens
Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions
Tools (4):
FastQC, BWA, SICER, IGV
Topics (5):
DNase-seq analysis, Homo sapiens, Mus musculus, Arthritis, Arterial Occlusive Diseases
Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites
Tools (5):
Bowtie, phantompeakqualtools, HOMER, BEDTools, SAMtools
Topics (8):
ChIP-seq analysis, RAD-seq analysis, WGS analysis, WES analysis, Amplicon sequencing analysis, Bacteria, Helicobacter pylori, Nucleotides
EED orchestration of heart maturation through interaction with HDACs is H3K27me3-independent
Tools (8):
STAR, RSEM, Bowtie, edgeR, Metascape, BWA, MACS, IGV
Topics (3):
RNA-seq analysis, DNase-seq analysis, Mus musculus
The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
Tools (3):
Bowtie2, MACS, Picard
Topics (3):
ChIP-seq analysis, Autoimmune Diseases, Neoplasms
Rice aleurone layer specific OsNF-YB1 regulates grain filling and endosperm development by interacting with an ERF transcription factor
Tools (6):
Bowtie2, MACS, DREME, TopHat, Cufflinks, BiNGO
Topics (9):
DNase-seq analysis, ChIP-seq analysis, RNA-seq analysis, sRNA-seq analysis, Oryza sativa, Ribonucleotides, Heterocyclic Compounds, 2-Ring, Purine Nucleotides, Amino Acids
Genome-wide chromatin and gene expression profiling during memory formation and maintenance in adult mice
Tools (5):
fastq-tools, Bowtie, RFECS, MACS, liftoveR
Topics (2):
ChIP-seq analysis, Brain Diseases
