codex.stemcells.cam.ac.uk
CODEXCODEX: a functional genomic portal developed by the Gottegens lab, Department of Haematology, University of Cambridge.
http://codex.stemcells.cam.ac.uk/
CODEX: a functional genomic portal developed by the Gottegens lab, Department of Haematology, University of Cambridge.
http://codex.stemcells.cam.ac.uk/
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CODEX | codex.stemcells.cam.ac.uk Reviews
https://codex.stemcells.cam.ac.uk
CODEX: a functional genomic portal developed by the Gottegens lab, Department of Haematology, University of Cambridge.
codex.stemcells.cam.ac.uk
CODEX
http://codex.stemcells.cam.ac.uk/about.php
Gene Set Control Analysis. This project presents a curated and comprehensible database of Next Generation Sequencing (NGS) experiments including ChIP-Seq, RNA-Seq and DNase-Seq. CODEX is a database of. Mouse and human experiments. Although, the main focus of CODEX is Haematopoiesis and Embryonic systems, the database includes a large variety of cell types. The main sources of the publicly available data within CODEX are taken from. Repositories such as GEO. The Gottgens lab - 2013.
CODEX
http://codex.stemcells.cam.ac.uk/doc_motif.php
Gene Set Control Analysis. De novo motif analysis was carried out on the central 100 bps of the peak regions using Homer. For any ChIP-Seq experiment in CODEX, all peak regions were used as input to the. Script in Homer. The program then looks for consensus sequences that are enriched in the sample relative to background (randomly selected sequences from the genome). The resulting HTML page and the motif position weight matrices (PWM) are displayed on CODEX. And Jolma et al. The Gottgens lab - 2013.
CODEX
http://codex.stemcells.cam.ac.uk/doc_gsca.php
Gene Set Control Analysis. Gene Set Control Analysis (GSCA). We have integrated Gene Set Control Analysis (GSCA) ( Joshi et al. Exp Hematol. 2013. 41(4):354-66. Within CODEX. This analysis provides a complementary computational approach to the routine Gene Ontology analysis. For an inputted gene set, the GSCA web tool identifies over-represented overlaps between the gene set and TF target genes by performing a hyper-geometric test to uncover potential transcriptional regulators. The Gottgens lab - 2013.
CODEX
http://codex.stemcells.cam.ac.uk/doc_similarity.php
Gene Set Control Analysis. The CODEX similarity analysis tool allows users to compare selected ChIP-Seq experiments peak profiles. We opted to compute similarity using the Dice coefficient. Instead of the traditional Pearson correlation. The Dice coefficient is designed to measure similarity between asymetric binary vectors. The Gottgens lab - 2013.
CODEX
http://codex.stemcells.cam.ac.uk/submit.php
Gene Set Control Analysis. If CODEX is missing a published or publicly available NGS experiment, please let us know by submitting the form below. All NGS data hosted on CODEX must be processed according to our pipeline and once published, will be transferred to the public domain of CODEX. The Gottgens lab - 2013.
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Gene Set Control Analysis. A comprehensive and functional compendium of Next Generation Sequencing experiments. CODEX provides access to processed and curated. Experiments, including ChIP-Seq (transcription factors and histones), RNA-Seq and DNase-Seq. To use CODEX: ( i. Select a specialized repository (HAEMCODE or ESCODE) or choose the whole compendium (CODEX), then ( ii. Filter by organism and ( iii. Choose how to explore the database. The specialised Haematopoietic Cell compendium of.
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