November 1, 2022
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bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:26:21
October 17, 2022
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Version number fixed Merge branch 'master' of

seriph78 authored on 17/10/2022 15:00:09
October 16, 2022
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Changed version number to 1.1.1

Silvia Giulia Galfre authored on 16/10/2022 14:03:19
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Removed the dependency from Python.

Silvia Giulia Galfre authored on 16/10/2022 10:21:09
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Removed the dependency from Python. The PCA function used is no longer basilisk/reticulate based but uses the irlba package. The test for PCA changed to be more robust and independent from rotations.

Silvia Giulia Galfre authored on 16/10/2022 10:21:09
April 26, 2022
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bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 16:20:54
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bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 16:20:54
March 29, 2022
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Ready for push to Bioconductor. Back compatibility for coex matrix added. Removed some warning and notes from checks (both Bioconductor and R). Specific files for est.min.parameters, and extract.coex functions

seriph78 authored on 29/03/2022 10:40:01
March 24, 2022
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COEX estimation faster and specific files for get.pval and get.GDI. Create specific file for functions get.pval and get.GDI. These two functions are also corrected for the new COEX storage. Changed the COEX estimation using only one observed matrix (instead of 4). Documenation for the two function vec2mat and mat2vec crated. New tests and test dataset checked and fixed. Plot_heatmap fixed. Change version 0.99.12

seriph78 authored on 24/03/2022 10:13:14
March 23, 2022
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New coex evaluation and storage implemented. In this new version the coex values are stored as a two dimension list: “genes” with all the gene names and “coex.values” with all unique values. To restore the dataframe (whole or partial) the function vec2mat_rfast is used. Updated also the get.coex_test (removed the old coex.RDS file from the test files). Fixed a bud in the vec2mat_rfast function (there was a problem with the creation of the partial matrix).

seriph78 authored on 23/03/2022 10:15:24
March 22, 2022
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COEX storage optimization The two function to convert the coex matrix into a list (coex vector and gene names vector) are modified to store only ones the gene names. The function vect2mat_rfast convert the two-item list into the complete coex matrix (if genes="all") or into a matrix of g x n with in the columns the desired genes and with all other genes (n) in the rows. Functions get.coex and moved from COTAN_main.R to their own files.

seriph78 authored on 22/03/2022 11:02:08
March 19, 2022
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Functions to convert named vector to symmetric matrix and the other way round. I created the two new functions to convert a named vector to a symmetric matrix with row and column names and a symmetric matrix to a vector (half size) keeping the row and column names. This will be used to estimate and store the coex in a more efficient and light way.

seriph78 authored on 19/03/2022 09:36:05
January 19, 2022
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Functions split started. We started to split function in different files. Some minor correction on automatic cotan structure creation (specially to improve the runability and make it lighter on RAM usage)

seriph78 authored on 19/01/2022 17:18:14
December 28, 2021
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Added cluster_homogeneity, cotan_on_cluster_DE and get.subset

Silvia Giulia Galfre authored on 26/12/2021 17:29:58 • seriph78 committed on 28/12/2021 17:44:08
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Added cotan_on_cluster_DE to detect an enrichment or depletion of a cluster for a specific gene compared with its complementary set (all other cells). It returns a list formed by a coex matrix (all clusters in the columns and all genes in rows) and a p-values matrix.

Silvia Giulia Galfre authored on 26/04/2021 08:12:33 • seriph78 committed on 28/12/2021 17:09:53