Man pages for CshlSiepelLab/tuSelecter2
Deconvolution of Expression for Nascent RNA Sequencing Data

add_dataAdd data
apply_bigwig_seqinfoApply seqinfo from bigwig to GRanges
apply_shape_profileChange shape of transcript models Create a...
assert_chromosome_existsAssert chromosome exists
cache_create_dirCreate local cache
cache_defaultsCreate cache defaults
cache_get_dirGet local cache path
cache_set_dirSet local cache path
collect_tss_featuresGenerate GRangesList of windows
covered_basesGets per-query coverage
create_binsCreate bins for multiple groups of overlapped transcripts
create_model_masksCreate model masks
create_transcript_modelsCreate transcript models
download_txdbDownload transcript model from biomart
fitFit model
gene_abundanceView gene abundances
get_abundanceretrieve abundance for plotting
get_dataGet data
get_masksGet target masks
get_transcribed_regionsAnnotates transcribed regions
get_transcriptsGet target transcripts
get_tx_idget_tx_id
group_trancript_modelsGroup transcripts
group_transcriptsGroup transcripts
is_length_two_vectoris_length_two_vector
is_matrix_listis_matrix_list
is_strand_vectoris_strand_vector
is_vector_listis_vector_list
labeled_feature_setBuild labeled data set
label_transcriptsGenerate training labels for TSS
list_cached_txdbView cache
load_txdbLoad txdb from cache
locus_statisticslocus_statistics
locus_variance_explainedlocus_variance_explained
mask_dataMask data
mask_transcriptsMask transcripts
matrix_list_dim_equalmatrix_list_dim_equal
model_agreementComputes GOF statistic for groups of transcripts
plot_modelPlot transcript_abundance object
predict_inactive_transcriptsReturn list of inactive TSS
predict_locusPredicts signal at locus level
predict_transcriptspredict_transcripts
reduce_transcript_modelsReduce transcript models
rescale_fixed_width_positionTripartite linear rescaling
save_txdbCache a TxDb
seqvVectorized seq.default
set_datatrack_ylimSet datatrack ylim
show-transcript_quantifier-methodShow an Object
split_pathSplit path
strip_loessSlims down loess object Removes parts of 'loess' object that...
summarize_bigwigSummarize bigwig
sum_squares_gradSum of squares gradient
sum_squares_lassoSum of squares
total_coverageTotal coverage
transcript_abundanceView transcript abundances
transcript_quantifiertranscript_quantifier
transcript_quantifier-classClass transcript_quantifier
transcript_quantifier_validtranscript_quantifier_valid
transcript_shape_profileCreates transcript_shape_profile
transcript_shape_profile-classClass transcript_shape_profile
tss_predictorTrain TSS activity predictor
tx_variance_explainedtx_variance_explained
upstream_polymerase_ratiodensity ratio calculation
viewView transcript shape profile View transcript shape model...
view_available_txdbRetrieve ensembl biomart
window_regionsGenerate GRangesList of windows
CshlSiepelLab/tuSelecter2 documentation built on July 18, 2021, 5:09 p.m.