gongx030/seatac
ATAC-seq V-plot analysis

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Man pages for gongx030/seatac
ATAC-seq V-plot analysis

add_genomic_featuresadd_genomic_features
add_genomic_features-Vplots-GRangesList-methodadd_genomic_features
add_genomic_features-Vplots-GRanges-methodadd_genomic_features
beta_schedulebeta_schedule
block_centerblock_center
cbind-Vplots-methodBinding Vplots objects column-wise
count_readscount_reads
count_reads_corecount_reads_core
count_reads-GRanges-character-BSgenome-methodCount reads
count_reads-GRangesList-character-BSgenome-methodCount reads
cut_datacut data
dim-Vplots-methoddim-Vplots
downsample_vplotdownsample_vplot
fitfit
fit-VaeModel-list-methodfit
fit-VaeModel-tf_dataset-methodfit
fit-VaeModel-VplotsList-methodfit
fit-VaeModel-Vplots-methodfit
get_fragment_size_per_batchget_fragment_size_per_batch
get_nucleosome_diffget_nucleosome_diff
get_nucleosome_scoreget_nucleosome_score
kernel_smoothing_1dkernel_smoothing_1d
load_modelload_model
load_model-VaeModel-methodload_model
Model-classModel
ncol-Vplots-methodnol-Vplots
predictpredict
predict_fragment_sizepredict_fragment_size
predict_fragment_size-VaeModel-Vplots-methodpredicted_fragment_size
predict-VaeModel-VplotsList-methodpredict
predict-VaeModel-Vplots-methodpredict
predict_vplotspredict_vplots
prepare_dataprepare_data
prepare_data-VaeModel-VplotsList-methodprepare_data
prepare_data-VaeModel-Vplots-methodprepare_data
read_aggregated_vplotread_aggregated_vplot
read_aggregated_vplot-GRangesList-character-BSgenome-methodRead aggregated V-plot from a list of genomic ranges...
read_bamread_bam
read_bam-character-GRanges-BSgenome-methodRead BAM file
read_bam-character-missing-BSgenome-methodRead BAM file
read_fragment_size_profileread_fragment_size_profile
read_fragment_size_profile-GRanges-character-BSgenome-methodRead fragment size profile
read_fragment_size_profile-missing-character-BSgenome-methodRead fragment size profile
read_vplotread_vplot
read_vplot_coreRead the V-plot
read_vplot-GRanges-character-BSgenome-methodRead the V-plot
read_vplot-GRangesList-character-BSgenome-methodRead the V-plot
resize-Vplots-methodResize Vplots
resultsresults
results_nucleosomeresults_nucleosome
results_phaseresults_phase
results-VaeModel-Vplots-methodresults
results_vplotsresults_vplots
scale01scale01
scale01-dgCMatrix-methodscale01
scale01-matrix-methodscale01
scale01-numeric-methodscale01
scale01-tensorflow.tensor-methodscale01
scale_vplotscale_vplot
seatacseatac: A package for ATAC-seq V-plot analysis
show-VplotsList-methodshow-VplotsList
show-Vplots-methodshow-Vplots
slidingWindows-Vplots-methodslidingWindows
split_datasetsplit_dataset
standarize_1dstandarize_1d
subset-Vplots-ANY-ANY-Vplots-methodSubsetting a Vplots object
sub-Vplots-ANY-ANY-ANY-methodSubsetting a Vplots object
until_out_of_range2Execute code that traverses a dataset until an out of range...
VaeModelVaeModel
VaeModel-classVaeModel
validatevalidate
validate_bamvalidate_bam
validate-VaeModel-VplotsList-methodvalidate
validate-VaeModel-Vplots-methodvalidate
vplotvplot
vplot_corevplot_core
Vplots-classVplots
VplotsList-classVplotsList
vplot-Vplots-methodvplot
WarmUpAndCosineDecayWarmup and cosine decay scheduler, the schedular used in the...
gongx030/seatac documentation built on April 15, 2023, 5:53 a.m.

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