New version of rGADEM - ChIP-Seq, de novo motif discovery
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Charles Joly ▴ 10
Last seen 7.3 years ago
Dear all, rGADEM is a de novo motif discovery tool for large scale genomic data that is part of an integrated pipeline for ChIP-seq analysis (PICS/rGADEM/MotIV) [1]. The program uses openMP in order to greatly reduce some parts of the calculation. We are proud to announce a new version of the software, rGADEM 2.0. The code is now up-to-date with the latest changes in the GADEM, the c version of the program. Notably, two new parameters have been introduced: nmotifs and maskR. With nmotifs, it is now possible to stop the analysis once a fixed amount of motifs have been found. With the maskR option, low-complexity sequences (i.e.: “aaaaaa”, “cacacaca”, etc) are ignored during the analysis. rGADEM 2.0 is now available in the devel section of bioconductor and should be available very soon in the release section. Do not hesitate to contact us directly or through the mailing list if you have any questions! Best regards, Charles Joly Beauparlant. [1] Mercier E., Droit A., Leping L. et al, 2010, An Integrated Pipeline for the Genome-Wide Analysis of Transcription Factor Binding Sites from ChIP-seq. [[alternative HTML version deleted]]
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