Tweak install #4
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…c site switch probabilities
…nces, now the input X should include both observed counts and NB expectation/BB total counts
…allow input argument to initialize log_mu and p_binom
…runtime of BetaBinom fitting, selecting obs with a high expectation in E step
… step optimization (only using data points with > threshold E step expectation)
…y unique values + number occurrences
…inding integer copynumber for each HMM state
… probability to enforce reference-based phasing more
…length difference affected by CNV
…F signals to refine clones
…lmixture_04 version
…length binning by a UMI count threshold). This gives _01 outputs
This reverts commit 5fc50e4.
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