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DCLEAR  

Distance Based Cell Lineage Reconstruction
View on CRAN: Click here


Download and install DCLEAR package within the R console
Install from CRAN:
install.packages("DCLEAR")

Install from Github:
library("remotes")
install_github("cran/DCLEAR")

Install by package version:
library("remotes")
install_version("DCLEAR", "1.0.13")



Attach the package and use:
library("DCLEAR")
Maintained by
Il-Youp Kwak
[Scholar Profile | Author Map]
First Published: 2021-07-15
Latest Update: 2023-09-14
Description:
R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020. References: Gong et al. (2021) , Gong et al. (2022) .
How to cite:
Il-Youp Kwak (2021). DCLEAR: Distance Based Cell Lineage Reconstruction. R package version 1.0.13, https://cran.r-project.org/web/packages/DCLEAR. Accessed 31 Mar. 2025.
Previous versions and publish date:
1.0.0 (2021-07-15 09:30), 1.0.8 (2021-09-03 13:40), 1.0.11 (2022-11-30 12:00), 1.0.12 (2023-02-16 17:00)
Other packages that cited DCLEAR R package
View DCLEAR citation profile
Other R packages that DCLEAR depends, imports, suggests or enhances
Complete documentation for DCLEAR
Functions, R codes and Examples using the DCLEAR R package
Some associated functions: DCLEAR . WH . WH_train . WH_train_fit . add_deletion . add_dropout . as_igraph-data.frame-method . as_igraph-phylo-method . as_igraph . as_lineage_tree-phyDat-phylo-lineage_tree_config-method . as_lineage_tree . as_phylo-igraph-method . as_phylo . dist_kmer_replacement_inference . dist_replacement-phyDat-kmer_summary-integer-method . dist_replacement-phyDat-missing-integer-method . dist_replacement . dist_weighted_hamming-phyDat-numeric-method . dist_weighted_hamming . downsample-igraph-method . downsample-lineage_tree-method . downsample . get_distance_prior . get_leaves-lineage_tree-method . get_leaves . get_node_names . get_replacement_probability . get_sequence . get_transition_probability . lineages . positional_mutation_prob . process_sequence-phyDat-method . process_sequence . prune-igraph-method . prune-lineage_tree-method . prune . random_tree . rbind-phyDat-method . sample_mutation_outcome . sample_mutation_site . sample_outcome_prob . score_simulation . sim_seqdata . simulate-lineage_tree_config-missing-method . simulate-lineage_tree_config-phyDat-method . simulate . simulate_core . substr_kmer-kmer_summary-method . substr_kmer . subtract-lineage_tree-lineage_tree-method . subtract . subtree-lineage_tree-method . subtree-phylo-method . subtree . summarize_kmer-phyDat-method . summarize_kmer . summarize_kmer_core . 
Some associated R codes: RcppExports.R . WH.R . sim_seq.R .  Full DCLEAR package functions and examples
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