BTR: Training and Analysing Asynchronous Boolean Models

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

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

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

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

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