BTR: Training and Analysing Asynchronous Boolean Models

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

Install the latest version of this package by entering the following in R:
install.packages("BTR")
AuthorChee Yee Lim
Date of publication2016-09-17 18:03:21
MaintainerChee Yee Lim <cyl49@cam.ac.uk>
LicenseGPL-3
Version1.2.4

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

Functions

amat_to_bm Man page
bm_to_amat Man page
bm_to_df Man page
bon_bmodel Man page
bon_istate Man page
BoolModel Man page
BoolModel-class Man page
BTR Man page
BTR-package Man page
calc_mscore Man page
calc_roc Man page
check_and Man page
compress_bmodel Man page
decompress_bmodel Man page
decreate_boolmodel Man page
df_to_bm Man page
emodel1 Man page
emodel2 Man page
emodel3 Man page
eval_bool Man page
extract_term Man page
filter_dflist Man page
gen_one_rmodel Man page
gen_singlerule Man page
gen_two_rmodel Man page
gen_two_rmodel_dag Man page
get_encodings Man page
grow_bmodel Man page
initialise_data Man page
initialise_model Man page
initialise_raw_data Man page
krum_bmodel Man page
krum_istate Man page
man_dist Man page
match_term Man page
minmod_internal Man page
minmod_model Man page
model_consensus Man page
model_dist Man page
model_setdiff Man page
model_train Man page
outgenysis_model Man page
outgraph_model Man page
outstate_graph Man page
plotBM Man page
printBM Man page
rcpp_simulate Man page
rcpp_validate Man page
simulate_model Man page
unique_raw_data Man page
validate_adjmat Man page
vcat Man page
which.random.min Man page
wilson_raw_data Man page
wilson_raw_rnaseq Man page
writeBM Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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