NEWS.md

In davismcc/cardelino: Clone Identification from Single Cell Data

News for Package cardelino

Changes in v0.99.3

• Changes to prepare package for submission to Bioconductor. (No functional changes)

Changes in v0.6.4 (21/08/2019)

• Fix bug in devianceIC() = D_post + 2 * p_D; and add both the original p_D, i.g., D_mean - D_post and the Gelman's alternative p_D = 2 * var(D). By default, DIC uses Gelman's method.
• Suggest narrowing theta1 for cardelino-free, e.g., prior1=c(45, 55)
• Add get_logLik() function to get log likelihood for clone_id_Gibbs(), namely P(A, D | C, I, theta0, theta1)

Changes in v0.6.3 (19/08/2019)

• Add devianceIC() for Deviance information criterion (DIC) for clone_id_Gibbs()
• Change the default of relax_Config=TRUE for clone_id() and clone_id_Gibbs()

Changes in version 0.6.2

• Fix the bug in Geweke_Z function for convergence diagnostic
• Change the default number of iterations in clone_id to 5000
• Add more tests

Changes in version 0.6.1

• Change the default colMatch to greedy search
• Rename the cell_assign_Gibbs to clone_id_Gibbs
• Rename the cell_assign_EM to clone_id_EM
• Move get_tree from clone_id.R to tree_utils.R
• Remove "Bernoulli" model in both clone_id_EM and clone_id_Gibbs. The user can transfer the binomial to Bernoulli by setting a threshold beforehand
• Remove the A_germ and D_germ parameters, leave it to future development to jointly modelling the germline variants
• Remove function load_vcf_h5 and dependency hdf5r

Changes in version 0.6.0

• Remove donor id relevant information and backup donor_id into v0.4.2 and a new branch with_vireo
• Remove donor_id.R, bin/run_vireo.R
• Remove tests/testthat/test-donorid.R, vignette/vignette-vireo.Rmd
• Remove unnecessary logo photos in inst

Changes in version 0.4.2

• Add binaryROC function of ROC curve
• Add message for switch vireo to Python implementation

Changes in version 0.4.1

• Support direct loading sparse matrix from cellSNP file in hdf5 format

Changes in version 0.4.0

• Support multiple chains when running clone_id (one chain by default)
• Support relabel during Gibbs sampling when running clone_id (not in use by default)
• Change sim_read_count: the default of wise0 is to "element", i.e., sequencing error rate is both variant and cell specific. Also, a new parameter sample_cell is added for the option to turn off sampling cells from seed D
• Change heat_matrix for supporting rownames and colnames matching the original order in the matrix instead of alphabetical order

Changes in version 0.3.9

• Add a runnable R file: run_vireo.R in /bin to run from command line
• Change load_GT_vcf by supporting GP for genotype probability
• Change load_cellSNP_vcf by supporting GL for genotype likelihood
• Change heat_matrix to for scale_x_discrete by default

Changes in version 0.3.8

• Change the convergence diagnosis in cell_assign_Gibbs to all cells
• Change the donor_read_simulator to beta-binomial for each variant in each cell

Changes in version 0.3.7

• Fix a bug in colMatch in force mode
• Specify the fixed relax rate in cell_assign_Gibbs, which can be used to turn the input Config as a uniform prior when setting relax_rate_fixed=0.5

Changes in version 0.3.4

• Add averaged Config_prob and relax_rate in cell_assign_Gibbs outputs
• Add force option in colMatch function to force one-to-one match

Changes in version 0.3.3

• Fix the bug in inferring the relax_rate in cell_assign_Gibbs

Changes in version 0.3.2

• Supporting learning the relax rate on clone configuration automatically

Changes in version 0.3.1

• fix the clone id missing for prob_mat.
• change the default the sampling iteration to 3000.

Changes in version 0.3.0

• cell_assign_Gibbs supports updating clone Configuration now. Set relax_Config between 0 and 1.
• change the default parameters for beta prior to better represent allelic dropout and imbalance in scRNA-seq data. It involves functions: sim_read_count, donor_read_simulator, and cell_assign_Gibbs
• minor change of pub.theme: title will be plain rather than bold.

Changes in version 0.2.7

• vireo supports match SNP from donor_data to cell_data; change default number of processors to n_proc=1
• change load_cellSNP_vcf default parameters to support more general case
• add more dependency to pass tests
• correct test-donor_id.R
• remove vignette-donorid.Rmd vignette and correct vignette-vireo.Rmd

Changes in version 0.2.5

• change donor_id to vireo
• fix minor bug for n_vars in vireo (i.e., donor_id)
• add vignette for demultiplexing without genotype
• change assessment for doublet detection indicator to prob_doublet

Changes in version 0.1.0

• add examples and remove unnecessary functions to pass biocCheck

davismcc/cardelino documentation built on Nov. 19, 2022, 2:44 a.m.