Nb convert param#7

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Congm12 wants to merge 160 commits intomainfrom

nb_convert_param

Commits on May 6, 2022

Commits on May 18, 2022

add HMM with NB and BetaBinom emission probabilities and site-specific site switch probabilities
Congm12
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Commits on Jun 7, 2022

Commits on Jun 10, 2022

add user defined initialization for NB and BetaBinom mean; to reduce runtime of BetaBinom fitting, selecting obs with a high expectation in E step
Congm12
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Commits on Jun 17, 2022

adjust the M step convergence criteria; add a heuristic to speed up M step optimization (only using data points with > threshold E step expectation)
Congm12
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Commits on Jul 15, 2022

Commits on Jul 21, 2022

Commits on Sep 28, 2022

address the 0 issue in RDR signal; update the initialization in pipeline_baum_welch
Congm12
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Commits on Oct 6, 2022

add initialize HMM RDR in log/original space option; add gurobi for finding integer copynumber for each HMM state
Congm12
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Commits on Oct 13, 2022

a trick to speed up M step
Congm12
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Commits on Oct 19, 2022

add back hmm code with scalefactor; fix the directory naming issue in utils_IO
Congm12
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Commits on Oct 23, 2022

add an example data for running HMM
Congm12
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Commits on Oct 27, 2022

gaussian HMM + phase switch for hatchet2
Congm12
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Commits on Nov 29, 2022

update utility functions
Congm12
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Commits on Jan 22, 2023

a full pipeline for BAF-only clones followed by using both RDR and BAF signals to refine clones
Congm12
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Commits on Feb 9, 2023

filter DE genes, better integer copy number inference; leads to normalmixture_04 version
Congm12
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Commits on Apr 10, 2023

Fixed minor error in initialization_by_gmm method
MayaGupta27
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Commits on Apr 11, 2023

Commits on Jun 23, 2023

Commits on Jun 26, 2023

Commits on Jun 28, 2023

Commits on Jul 4, 2023

Commits on Jul 5, 2023

splitting clone spatial plot for supervised version into samples
Congm12
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Commits on Jul 6, 2023

addressing the NAN error when spaceranger outputs of different slices have different number of genes
Congm12
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Commits on Jul 11, 2023

add hatchet plotting and evaluation accuracy utility; fix bug related to dense matrix/sparse matrix
Congm12
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Commits on Jul 16, 2023

Commits on Jul 17, 2023

update post-thresholding of key events and highlighting in plots
Congm12
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Commits on Jul 26, 2023

Commits on Jul 31, 2023

fix an edge case of merging bins across chrs
Congm12
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Commits on Aug 3, 2023

Commits on Aug 10, 2023

update the integer copy number searching without ploidy constraint to first identify diploid state and then fit rdr and baf; add constraint that if rdr /baf deviation is too large, the state cannot…
Congm12
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Commits on Aug 13, 2023

Commits on Aug 15, 2023

Commits on Aug 16, 2023

import ploting utilities; multiple random initialization for initial integer copy numbers
Congm12
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Commits on Aug 20, 2023

add integer copy number approach by scale factor from diploid state; add try except for whether able to find diploid state in supervised mode
Congm12
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Commits on Aug 27, 2023

Commits on Oct 9, 2023

fix the error in merge pseudobulk about format of tumor proportion; update plotting
Congm12
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Commits on Oct 11, 2023

fix errors in edges cases; add more plotting functions
Congm12
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Commits on Oct 12, 2023

plotting 1d2d plots from dataframes
Congm12
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Commits on Oct 18, 2023

distribute transcript count of each gene to the overlapping bins proportional to length
Congm12
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Commits on Oct 21, 2023

Commits on Oct 23, 2023

fix bug in greedy binning; remove unused arguments in arg parse
Congm12
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Commits on Oct 24, 2023

Commits on Oct 25, 2023

Commits on Oct 26, 2023

remove nan of the input data frame in plotting function
Congm12
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Commits on Oct 28, 2023

include more integer to state conversions in plot_hatchet
Congm12
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Commits on Oct 30, 2023

Commits on Nov 1, 2023

Commits on Nov 2, 2023

Commits on Nov 7, 2023

Commits on Nov 8, 2023

organize directory structure; test running calicost in snakemake
Congm12
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Commits on Nov 16, 2023

update parameter specification
Congm12
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Commits on Nov 29, 2023

Commits on Nov 30, 2023

update tumor proportion estimation function
Congm12
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Commits on Dec 6, 2023

add inferring tumor proportion module (identify LOH states, estimate proportion by aggregating counts across all LOH regions per cell
Congm12
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Commits on Dec 7, 2023

Commits on Dec 30, 2023

estimate tumor proportion using LOH
Congm12
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Commits on Jan 20, 2024

update the high-purity clone and loh state selection threshold, now use one higher baf deviation threshold for both selections; move the filtering step of potential allele-specific expression bins …
Congm12
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Commits on Jan 23, 2024

Commits on Feb 5, 2024

minor adjustment on plotting and input parsing
Congm12
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Commits on Feb 15, 2024

Commits on Feb 18, 2024

Commits on Feb 19, 2024

merge change
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update docs
Congm12
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Commits on Feb 20, 2024

Commits on Feb 26, 2024

Commits on Mar 3, 2024

update readme paths for example data
Congm12
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Commits on Mar 15, 2024

fix an edge case
Congm12
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Commits on Apr 11, 2024

Commits on Apr 15, 2024

Commits on Jun 9, 2024

Commits on Jul 9, 2024

a more stable version of converting NB mean and dispersion to n and p parameters
Congm12
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Commits on Jul 11, 2024

switch to the more stable version in distribution fitting fun
Congm12
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