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A robust software package for quantitative comparison of ChIP-Seq data sets.

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• SciCrunch
• 13 years ago - by Anonymous

Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts.

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• SciCrunch
• 13 years ago - by Anonymous

A software for determining DNA/protein binding sites from a ChIP-Seq experiment.

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• SciCrunch
• 13 years ago - by Anonymous

Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments.

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• SciCrunch
• 13 years ago - by Anonymous

An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS).

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• SciCrunch
• 13 years ago - by Anonymous

Software for a multi-purpose ChIP Seq peak caller.

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• SciCrunch
• 13 years ago - by Anonymous

A software program to call peaks from ChIP-seq data for transcription factor binding sites.

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• SciCrunch
• 13 years ago - by Anonymous

Software developed as a flexible mixture modeling approach for detecting peaks of one-sample (ChIP sample) or two-sample (ChIP sample and matched control sample) ChIP-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris).

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• SciCrunch
• 13 years ago - by Anonymous

A Hidden Markov Model-based algorithm for the purpose of defining genome-wide ChIP-enriched peaks in the human genome using short sequence reads.

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• SciCrunch
• 13 years ago - by Anonymous

A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).

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• SciCrunch
• 13 years ago - by Anonymous

A Python package for doing RNA-seq and ChIP-seq (hence the dual-use).

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• SciCrunch
• 13 years ago - by Anonymous

A high resolution transcription factor binding site (TFBS) identification (deconvolution) algorithm. dPeak implements a probabilistic model that accurately describes ChIP-exo and ChIP-Seq data generation process for both the SET and PET assays.

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• SciCrunch
• 13 years ago - by Anonymous

A Plant MicroRNA Target Expression Database to study the microRNA (miRNA) functions by inferring their target gene expression profiles among the large amount of existing microarray data. You may also predict your miRNA targets and retrieve their microarray expression data.

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• SciCrunch
• 13 years ago - by Anonymous

Catalogs of predicted microRNA targets in worm (based on ce6 genome assembly), fly (dm3), mouse (mm9) and human (hg18). We follow standard seed parameter settings and consider seeds of length 6-8 bases, beginning at position 2 of the microRNA. No mismatches or loops are allowed, but a single G:U wobble is allowed in 7- or 8-mers. In genes missing a 3' UTR annotation, 500 bp (fly), 800 bp (human and mouse) or 300 bp (worm) downstream of the annotated end of the coding sequence were used as the predicted UTR. For each organism, a catalog with zero flank and with a flank of 3 and 15 bases upstream and downstream.

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• SciCrunch
• 13 years ago - by Anonymous

Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.

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• SciCrunch
• 13 years ago - by Anonymous

An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts.

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• SciCrunch
• 13 years ago - by Anonymous

A web-based tool used for homologous miRNA gene search in several species. The code is available on request.

• Resource
• SciCrunch
• 13 years ago - by Anonymous