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JAMM Downloads Archive
Latest JAMM releases (going back to JAMMv1.0.7rev2) can be found on the Github Release Page.
Versions older than JAMM1.0.7rev2 (including the version used in the publication JAMMv1.0.4rev1) can be found on this page.
Changelog: Clustering model initialization options now available, default is "deterministic" which is the same as v1.0.4rev1, other option is "stochastic" and is the same as to v1.0.5 and 1.0.6revX - k-means-initialized local window clustering when chromosome-wide clustering initialization fails - Ability to report enriched windows for which all clustering attempts fails (optional) - Seeding for any sampling/randomization step is done and reported in the command line - JAMM will not overwrite results if "peaks" or "xcorr" folders exist - JAMM will report the average read lengths in the command line - SignalGenerator.sh can handle paired-end files.
Changelog: fixed bash localization bug that affected peak scoring for users with "," as their decimal point bash setting.
Changelog: fixed various bugs in v1.0.6rev1 that caused paired-end option to not function.
Changelog: window fold enrichment added with "-e" - optional adjustment of the initialization mean vectors for every window - Background model correction for chromosomes with skewed background based on average of other chromosomes (when there is no biological control)- automatic window fold enrichment estimation "-e auto" - read length calculation consolidated in one section - removed dependencies on sqldf R package - removed JAMMxcorr - SignalGenerator has now background correction similar to JAMM.sh
Changelog: changed model structure determination by using (at most 20) randomly chosen windows from the top scoring quarter of windows - summit is determined without subtracting background, and using normalized-extended-read counts (NOT smoothed) - added paired-end functionality, via BEDPE files - added "window" option for "-r".
- JAMM v1.0.4rev1 - version used in publication
Changelog: fixed a bug with constructing read count profiles.
Changelog: SignalGenerator.sh can handle paired-end files - Clustering model initialization options now available, default is "deterministic" which is the same as v1.0.4rev1, other option is "stochastic" and is the same as to v1.0.5 and 1.0.6revX (see option -i) - k-means-initialized local window clustering when chromosome-wide clustering intialization fails - Ability to report enriched windows for which all clustering atempts failts (optional). Those windows will be flagged by "NoClust" in their name. - Seeding for any sampling/randomization step is done and reported in the command line, so that results could be exactly reproduced. - JAMM will not overwrite results if "peaks" or "xcorr" folders exist.- JAMM will report the average read lengths in the command line.
Changelog: window fold enrichment added with "-e" - optional adjustment of the initialization mean vectors for every window - Background model correction for chromosomes with skewed background based on average of other chromosomes (when there is no biological control)- automatic window fold enrichment estimation "-e auto"