BTR: Training and Analysing Asynchronous Boolean Models

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Tools for inferring asynchronous Boolean models from single-cell expression data.

Author
Chee Yee Lim
Date of publication
2016-09-17 18:03:21
Maintainer
Chee Yee Lim <cyl49@cam.ac.uk>
License
GPL-3
Version
1.2.4

View on CRAN

Man pages

amat_to_bm
Convert adjacency matrix into BoolModel object
bm_to_amat
Convert BoolModel into adjacency matrix
bm_to_df
Convert BoolModel object into BoolNet readable data frame
bon_bmodel
HSC Boolean Model from Bonzanni et al.
bon_istate
Initial state from Bonzanni et al.
BoolModel-class
An S4 class to represent a Boolean Model
BTR
BTR: A package for studying asynchronous Boolean models
calc_mscore
Calculating Boolean model score wrt to a dataset
calc_roc
Calculate precision, recall, f-score, accuracy and...
check_and
Check if containing AND terms
compress_bmodel
Compress BoolModel
decompress_bmodel
Decompress BoolModel
decreate_boolmodel
Decreate Boolean model
df_to_bm
Convert a data frame into BoolModel object
emodel1
Example Boolean Model used in the vignette
emodel2
Example Boolean Model used in the vignette
emodel3
Example Boolean Model used in the vignette
eval_bool
Evaluating Boolean rules
extract_term
Extract Boolean terms
filter_dflist
Filter columns of df in a list
gen_one_rmodel
Generate a random Boolean model
gen_singlerule
Generate random act and inh rule for a single gene
gen_two_rmodel
Generate two random Boolean models with a specified number of...
gen_two_rmodel_dag
Generate two random DAG Boolean models with a specified...
get_encodings
Get corresponding encodings for compression or decompression.
grow_bmodel
Add extra genes to a Boolean model
initialise_data
Initialise data
initialise_model
Initialise model
initialise_raw_data
Initialise raw data
krum_bmodel
Myeloid Boolean Model from Krumsiek et al.
krum_istate
Initial state from Krumsiek et al.
man_dist
Calculates pairwise Manhattan distances between two matrices
match_term
Check for matching terms
minmod_internal
Inner function of minimal modification of whole Boolean model
minmod_model
Minimal modification of whole Boolean model
model_consensus
Intersection of genes
model_dist
Calculate distance between Boolean models
model_setdiff
Find the set difference between two Boolean models
model_train
Training Model
outgenysis_model
Output a Boolean Model into Genysis readable format
outgraph_model
Output a Boolean Model into Cytoscape & Gephi readable format
outstate_graph
Generate state transition graph
plotBM
Plot Boolean Model
printBM
Print Boolean Model
rcpp_simulate
Simulate a Boolean model.
rcpp_validate
Calculating validation scores between two adjacency matrices
simulate_model
Simulating Boolean model
unique_raw_data
Remove raw data duplicated wrt to the model state
validate_adjmat
Calculate true positive, true negative, false positive and...
vcat
Verbose cat
which.random.min
Pick a random minimum value
wilson_raw_data
Raw single cell qRT-PCR expression data from Wilson et al.
wilson_raw_rnaseq
Raw single cell RNAseq expression data from Wilson et al.
writeBM
Write Boolean Model

Files in this package

BTR
BTR/inst
BTR/inst/CITATION
BTR/inst/doc
BTR/inst/doc/btr.Rmd
BTR/inst/doc/btr.R
BTR/inst/doc/btr.html
BTR/src
BTR/src/score_calculation.cpp
BTR/src/RcppExports.cpp
BTR/src/simulation.cpp
BTR/NAMESPACE
BTR/data
BTR/data/krum_bmodel.rda
BTR/data/krum_istate.rda
BTR/data/bon_bmodel.rda
BTR/data/wilson_raw_rnaseq.rda
BTR/data/bon_istate.rda
BTR/data/example_models.rda
BTR/data/datalist
BTR/data/wilson_raw_data.rda
BTR/R
BTR/R/data_desc.R
BTR/R/output_format.R
BTR/R/methods.R
BTR/R/simulation.R
BTR/R/general.R
BTR/R/btr.R
BTR/R/search.R
BTR/R/RcppExports.R
BTR/R/boolmodel_class.R
BTR/R/score_calculation.R
BTR/R/rand_model.R
BTR/R/compression.R
BTR/R/initialisation.R
BTR/R/model_modification.R
BTR/vignettes
BTR/vignettes/btr.Rmd
BTR/MD5
BTR/build
BTR/build/vignette.rds
BTR/DESCRIPTION
BTR/man
BTR/man/decompress_bmodel.Rd
BTR/man/amat_to_bm.Rd
BTR/man/BTR.Rd
BTR/man/emodel3.Rd
BTR/man/model_setdiff.Rd
BTR/man/gen_two_rmodel.Rd
BTR/man/man_dist.Rd
BTR/man/minmod_internal.Rd
BTR/man/initialise_raw_data.Rd
BTR/man/rcpp_simulate.Rd
BTR/man/outgenysis_model.Rd
BTR/man/model_consensus.Rd
BTR/man/krum_istate.Rd
BTR/man/filter_dflist.Rd
BTR/man/eval_bool.Rd
BTR/man/simulate_model.Rd
BTR/man/gen_two_rmodel_dag.Rd
BTR/man/wilson_raw_data.Rd
BTR/man/wilson_raw_rnaseq.Rd
BTR/man/bon_istate.Rd
BTR/man/decreate_boolmodel.Rd
BTR/man/outstate_graph.Rd
BTR/man/initialise_data.Rd
BTR/man/model_dist.Rd
BTR/man/unique_raw_data.Rd
BTR/man/krum_bmodel.Rd
BTR/man/check_and.Rd
BTR/man/writeBM.Rd
BTR/man/outgraph_model.Rd
BTR/man/validate_adjmat.Rd
BTR/man/gen_singlerule.Rd
BTR/man/bm_to_amat.Rd
BTR/man/which.random.min.Rd
BTR/man/emodel2.Rd
BTR/man/calc_mscore.Rd
BTR/man/model_train.Rd
BTR/man/bon_bmodel.Rd
BTR/man/minmod_model.Rd
BTR/man/vcat.Rd
BTR/man/BoolModel-class.Rd
BTR/man/get_encodings.Rd
BTR/man/grow_bmodel.Rd
BTR/man/initialise_model.Rd
BTR/man/printBM.Rd
BTR/man/extract_term.Rd
BTR/man/emodel1.Rd
BTR/man/df_to_bm.Rd
BTR/man/compress_bmodel.Rd
BTR/man/rcpp_validate.Rd
BTR/man/calc_roc.Rd
BTR/man/gen_one_rmodel.Rd
BTR/man/bm_to_df.Rd
BTR/man/match_term.Rd
BTR/man/plotBM.Rd