Showing 7 of total 7 results (show query)
bioc
motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.
Maintained by Jianhong Ou. Last updated 3 months ago.
sequencematchingvisualizationsequencingmicroarrayalignmentchipchipchipseqmotifannotationdataimport
7.93 score 188 scripts 6 dependentsbioc
sevenC:Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.
Maintained by Jonas Ibn-Salem. Last updated 5 months ago.
dna3dstructurechipchipcoveragedataimportepigeneticsfunctionalgenomicsclassificationregressionchipseqhicannotation3d-genomechip-seqchromatin-interactionhi-cpredictionsequence-motiftranscription-factors
12 stars 5.38 score 3 scriptsbioc
rGADEM:de novo motif discovery
rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.
Maintained by Arnaud Droit. Last updated 5 months ago.
microarraychipchipsequencingchipseqmotifdiscoveryopenmp
4.95 score 56 scriptsbioc
iChip:Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Hidden Ising models are implemented to identify enriched genomic regions in ChIP-chip data. They can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.
Maintained by Qianxing Mo. Last updated 5 months ago.
chipchiponechannelagilentchipmicroarray
4.15 score 3 scriptsbioc
les:Identifying Differential Effects in Tiling Microarray Data
The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.
Maintained by Julian Gehring. Last updated 5 months ago.
microarraydifferentialexpressionchipchipdnamethylationtranscription
3.78 score 3 scripts 1 dependentsbioc
ChIPXpress:ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
Maintained by George Wu. Last updated 5 months ago.
3.78 score 2 scripts