lapa
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Feature Overview:
Quick Start
LAPA
Running LAPA with CLI and python
CLI arguments
Output format
Quality Control (QC)
Statistical testing
API Reference
lapa
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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L
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M
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P
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R
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S
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T
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U
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V
Symbols
--abundance_input
lapa_correct_talon command line option
--abundance_output
lapa_correct_talon command line option
--alignment
lapa command line option
lapa_link_tss_to_tes command line option
lapa_tss command line option
--annotation
lapa command line option
lapa_tss command line option
--chrom_sizes
lapa command line option
lapa_tss command line option
--cluster_extent_cutoff
lapa command line option
lapa_tss command line option
--cluster_ratio_cutoff
lapa command line option
lapa_tss command line option
--cluster_window
lapa command line option
lapa_tss command line option
--counting_method
lapa command line option
--dataset
lapa_link_tss_to_tes command line option
--fasta
lapa command line option
lapa_tss command line option
--gtf_input
lapa_correct_talon command line option
--gtf_output
lapa_correct_talon command line option
--keep_unsupported
lapa_correct_talon command line option
--lapa_dir
lapa_link_tss_to_tes command line option
--lapa_tss_dir
lapa_link_tss_to_tes command line option
--links
lapa_correct_talon command line option
--mapq
lapa command line option
lapa_link_tss_to_tes command line option
lapa_tss command line option
--min_percent_a
lapa command line option
--min_read_length
lapa_link_tss_to_tes command line option
--min_replication_rate
lapa command line option
lapa_tss command line option
--min_tail_len
lapa command line option
--non_replicates_read_threhold
lapa command line option
lapa_tss command line option
--output
lapa_link_tss_to_tes command line option
--output_dir
lapa command line option
lapa_tss command line option
--read_annot
lapa_correct_talon command line option
--replication_min_count
lapa command line option
lapa_tss command line option
--replication_num_sample
lapa command line option
lapa_tss command line option
--replication_rolling_size
lapa command line option
lapa_tss command line option
_
__call__() (lapa.lapa._Lapa method)
__contains__() (lapa.correction.TranscriptModifier method)
__len__() (lapa.cluster.Cluster method)
__repr__() (lapa.cluster.Cluster method)
__str__() (lapa.cluster.Cluster method)
_agg_annotation_gene() (lapa.genomic_regions._GenomicRegions method)
_agg_per_groups() (lapa.result._LapaResult static method)
_calculate_tail_seq() (lapa.count.ThreePrimeCounter static method)
_core_cols (in module lapa.replication)
(in module lapa.result)
_count_arr() (lapa.cluster.Cluster static method)
_count_read_annot() (lapa.count.BaseMultiCounter method)
(lapa.count.TesMultiCounter method)
(lapa.count.TssMultiCounter method)
_GenomicRegions (class in lapa.genomic_regions)
_k_n() (lapa.result._LapaResult method)
_keep_cols (lapa.lapa.Lapa attribute)
(lapa.lapa.LapaTss attribute)
_Lapa (class in lapa.lapa)
_LapaResult (class in lapa.result)
_link_reads_to_tes() (in module lapa.link)
_link_reads_to_tss() (in module lapa.link)
_links_transcript_agg() (in module lapa.correction)
_read_alignment_reads() (in module lapa.link)
_read_cluster() (lapa.result._LapaResult method)
(lapa.result.LapaResult method)
(lapa.result.LapaTssResult method)
_read_is_tailed() (lapa.count.PolyaTailCounter method)
_read_talon_read_annot_five_prime_count() (in module lapa.utils.io)
_read_talon_read_annot_three_prime_count() (in module lapa.utils.io)
_read_talon_read_counts() (in module lapa.utils.io)
_reads_cols (in module lapa.link)
_save_corrected_gtf() (in module lapa.correction)
_set_index() (lapa.result._LapaResult method)
_sort_gtf() (lapa.correction.TranscriptModifier static method)
_sort_gtf_key() (lapa.correction.TranscriptModifier static method)
_to_bigwig() (lapa.count.BaseCounter static method)
(lapa.count.BaseMultiCounter static method)
_tqdm_clustering() (in module lapa.cluster)
_tqdm_counting() (in module lapa.count)
_tqdm_pandas_gr() (in module lapa.genomic_regions)
_transcript_tss_tes() (in module lapa.correction)
_update_abundace() (in module lapa.correction)
A
add_transcript() (lapa.correction.TranscriptModifier method)
agg_sample_cols() (in module lapa.replication)
aggregate_samples() (lapa.lapa._Lapa class method)
annotate() (lapa.genomic_regions._GenomicRegions method)
annotate_cluster() (lapa.lapa._Lapa method)
annotated_site() (lapa.genomic_regions._GenomicRegions method)
(lapa.genomic_regions.PolyAGenomicRegions method)
(lapa.genomic_regions.TssGenomicRegions method)
attribute() (lapa.result._LapaResult method)
B
bam (lapa.count.BaseCounter attribute)
(lapa.count.BaseCounter property)
(lapa.count.FivePrimeCounter attribute)
(lapa.count.PolyaTailCounter attribute)
(lapa.count.ThreePrimeCounter attribute)
BaseCounter (class in lapa.count)
BaseMultiCounter (class in lapa.count)
beta_binomial_test() (lapa.result._LapaResult method)
build_counter() (lapa.count.BaseMultiCounter method)
(lapa.count.TesMultiCounter method)
(lapa.count.TssMultiCounter method)
bw_from_pyranges() (in module lapa.utils.io)
C
calculate_usage() (lapa.lapa._Lapa static method)
cli_lapa() (in module lapa.main)
cli_lapa_correct_talon() (in module lapa.main)
cli_lapa_link_tss_to_tes() (in module lapa.main)
cli_lapa_tss() (in module lapa.main)
Cluster (class in lapa.cluster)
(lapa.cluster.Clustering attribute)
(lapa.cluster.PolyAClustering attribute)
(lapa.cluster.TssClustering attribute)
cluster() (lapa.cluster.Clustering method)
cluster_col_order (in module lapa.utils.io)
cluster_path (lapa.result._LapaResult property)
Clustering (class in lapa.cluster)
clustering() (lapa.lapa._Lapa method)
copy() (lapa.correction.Transcript method)
correct_talon() (in module lapa.correction)
count() (lapa.count.BaseCounter method)
count_dir (lapa.result._LapaResult property)
count_read() (lapa.count.BaseCounter method)
(lapa.count.FivePrimeCounter method)
(lapa.count.ThreePrimeCounter method)
counting() (lapa.lapa._Lapa method)
counts() (lapa.result._LapaResult method)
create_clustering() (lapa.lapa._Lapa method)
(lapa.lapa.Lapa method)
(lapa.lapa.LapaTss method)
create_counter() (lapa.lapa._Lapa method)
(lapa.lapa.Lapa method)
(lapa.lapa.LapaTss method)
create_genomic_regions() (lapa.lapa._Lapa method)
(lapa.lapa.Lapa method)
(lapa.lapa.LapaTss method)
D
dataset_dir (lapa.lapa._Lapa property)
(lapa.result._LapaResult property)
dataset_path (lapa.result._LapaResult property)
datasets (lapa.result._LapaResult property)
detect_polyA_tail() (lapa.count.PolyaTailCounter static method)
E
extend() (lapa.cluster.Cluster method)
F
features() (lapa.genomic_regions._GenomicRegions method)
fetch_transcript() (lapa.correction.TranscriptModifier method)
filter_read() (lapa.count.BaseCounter method)
(lapa.count.PolyaTailCounter method)
filter_replication() (lapa.lapa._Lapa method)
fisher_exact_test() (lapa.result._LapaResult method)
five_prime_exon_idx (lapa.correction.Transcript property)
FivePrimeCounter (class in lapa.count)
fraction_A() (lapa.cluster.PolyACluster method)
G
gene_id() (lapa.result._LapaResult method)
get_tes_from_gtf() (in module lapa.utils.gtf)
get_tss_from_gtf() (in module lapa.utils.gtf)
I
intergenic_genes() (lapa.genomic_regions._GenomicRegions method)
iter_reads() (lapa.count.BaseCounter method)
iter_tailed_reads() (lapa.count.PolyaTailCounter method)
L
lapa
module
Lapa (class in lapa.lapa)
lapa command line option
--alignment
--annotation
--chrom_sizes
--cluster_extent_cutoff
--cluster_ratio_cutoff
--cluster_window
--counting_method
--fasta
--mapq
--min_percent_a
--min_replication_rate
--min_tail_len
--non_replicates_read_threhold
--output_dir
--replication_min_count
--replication_num_sample
--replication_rolling_size
lapa() (in module lapa)
(in module lapa.lapa)
lapa.cluster
module
lapa.correction
module
lapa.count
module
lapa.genomic_regions
module
lapa.lapa
module
lapa.link
module
lapa.main
module
lapa.replication
module
lapa.result
module
lapa.utils
module
lapa.utils.common
module
lapa.utils.gtf
module
lapa.utils.io
module
lapa_correct_talon command line option
--abundance_input
--abundance_output
--gtf_input
--gtf_output
--keep_unsupported
--links
--read_annot
lapa_link_tss_to_tes command line option
--alignment
--dataset
--lapa_dir
--lapa_tss_dir
--mapq
--min_read_length
--output
lapa_tss command line option
--alignment
--annotation
--chrom_sizes
--cluster_extent_cutoff
--cluster_ratio_cutoff
--cluster_window
--fasta
--mapq
--min_replication_rate
--non_replicates_read_threhold
--output_dir
--replication_min_count
--replication_num_sample
--replication_rolling_size
lapa_tss() (in module lapa)
(in module lapa.lapa)
LapaResult (class in lapa.result)
LapaTss (class in lapa.lapa)
LapaTssResult (class in lapa.result)
link_tss_to_tes() (in module lapa)
(in module lapa.link)
M
make_logs() (lapa.lapa._Lapa method)
module
lapa
lapa.cluster
lapa.correction
lapa.count
lapa.genomic_regions
lapa.lapa
lapa.link
lapa.main
lapa.replication
lapa.result
lapa.utils
lapa.utils.common
lapa.utils.gtf
lapa.utils.io
P
pad_series() (in module lapa.utils.common)
peak() (lapa.cluster.Cluster method)
plot_replication_rate() (lapa.result._LapaResult method)
plot_tail_len_dist() (lapa.count.PolyaTailCounter method)
polyA_signal_seqs (in module lapa.utils.common)
polyA_signal_sequence() (lapa.cluster.PolyACluster method)
polyA_site() (lapa.cluster.PolyACluster method)
PolyACluster (class in lapa.cluster)
PolyAClustering (class in lapa.cluster)
PolyAGenomicRegions (class in lapa.genomic_regions)
PolyaTailCounter (class in lapa.count)
prepare_alignment() (lapa.lapa._Lapa method)
R
raw_sample_dir (lapa.lapa._Lapa property)
read_chrom_sizes() (in module lapa.utils.io)
read_clusters() (lapa.result._LapaResult method)
(lapa.result.LapaResult method)
read_counts() (lapa.result._LapaResult method)
read_dataset() (lapa.result._LapaResult method)
read_polyA_cluster() (in module lapa)
(in module lapa.utils.io)
read_sample() (lapa.result._LapaResult method)
read_talon_read_annot() (in module lapa.utils.io)
read_talon_read_annot_five_prime_count() (in module lapa.utils.io)
read_talon_read_annot_three_prime_count() (in module lapa.utils.io)
read_tss_cluster() (in module lapa)
(in module lapa.utils.io)
replication_dataset() (in module lapa.replication)
replication_rate() (in module lapa.replication)
(lapa.result._LapaResult method)
S
sample_cluster() (lapa.lapa._Lapa method)
(lapa.lapa.Lapa method)
sample_dir (lapa.lapa._Lapa property)
(lapa.result._LapaResult property)
samples (lapa.result._LapaResult property)
save_cluster() (lapa.lapa._Lapa method)
save_clusters() (lapa.lapa._Lapa method)
save_count_bw() (in module lapa.count)
save_datasets() (lapa.lapa._Lapa method)
save_samples() (lapa.lapa._Lapa method)
save_tailed_reads() (lapa.count.PolyaTailCounter method)
save_tes_count_bw() (in module lapa.count)
save_tss_count_bw() (in module lapa.count)
T
tail_len_dist() (lapa.count.PolyaTailCounter method)
TesMultiCounter (class in lapa.count)
three_prime_exon_idx (lapa.correction.Transcript property)
ThreePrimeCounter (class in lapa.count)
to_bigwig() (lapa.count.BaseCounter method)
to_df() (lapa.cluster.Clustering method)
(lapa.count.BaseCounter method)
(lapa.count.BaseMultiCounter method)
to_dict() (lapa.cluster.Cluster method)
(lapa.cluster.PolyACluster method)
(lapa.cluster.TssCluster method)
to_gr() (lapa.count.BaseCounter method)
to_gtf() (lapa.correction.TranscriptModifier method)
total_count (lapa.cluster.Cluster property)
total_counts() (lapa.result._LapaResult method)
Transcript (class in lapa.correction)
TranscriptModifier (class in lapa.correction)
tss_cluster_col_order (in module lapa.utils.io)
TssCluster (class in lapa.cluster)
TssClustering (class in lapa.cluster)
TssGenomicRegions (class in lapa.genomic_regions)
TssMultiCounter (class in lapa.count)
U
update_polyA_site() (lapa.correction.Transcript method)
update_tss_site() (lapa.correction.Transcript method)
V
valid_five_prime_exon_len() (lapa.correction.Transcript method)
valid_three_prime_exon_len() (lapa.correction.Transcript method)
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