Index

A

add_legends() (lcdblib.plotting.results_table.MarginalHistScatter method) align_with() (lcdblib.plotting.results_table.ResultsTable method) append() (lcdblib.plotting.results_table.MarginalHistScatter method)

arguments() (in module lcdblib.utils.chrom_convert) attach_db() (lcdblib.plotting.results_table.ResultsTable method) autosql_file() (lcdblib.plotting.results_table.DESeqResults method)

B

boolean_labels() (in module lcdblib.utils.utils)

bowtie2_index_from_prefix() (in module lcdblib.snakemake.aligners) build_targets() (lcdblib.snakemake.interface.SampleHandler method)

C

cartesian_product() (in module lcdblib.pandas.utils) changed() (lcdblib.plotting.results_table.DifferentialExpressionResults method) cmap_center_adjust() (in module lcdblib.plotting.colormap_adjust) cmap_center_point_adjust() (in module lcdblib.plotting.colormap_adjust) cmap_powerlaw_adjust() (in module lcdblib.plotting.colormap_adjust)

color_test() (in module lcdblib.plotting.colormap_adjust) colormapped_bedfile() (lcdblib.plotting.results_table.DESeqResults method) convertFeature() (in module lcdblib.utils.chrom_convert) copy() (lcdblib.plotting.results_table.ResultsTable method) corrfunc() (in module lcdblib.plotting.basic)

D

DESeq2Results (class in lcdblib.plotting.results_table) DESeqResults (class in lcdblib.plotting.results_table)

DifferentialExpressionResults (class in lcdblib.plotting.results_table) display() (lcdblib.images.SVG.nb_svg method) downregulated() (lcdblib.plotting.results_table.DifferentialExpressionResults method)

E

EdgeRResults (class in lcdblib.plotting.results_table)

extract_wildcards() (in module lcdblib.snakemake.helpers)

F

fasta_convert() (in module lcdblib.utils.chrom_convert) FastQC (class in lcdblib.parse.fastqc) FastQCBlock (class in lcdblib.parse.fastqc) features() (lcdblib.plotting.results_table.ResultsTable method) fill_patterns() (in module lcdblib.snakemake.helpers)

filter() (lcdblib.logger.InfoFilter method) find_level() (lcdblib.snakemake.interface.SampleHandler method) find_sample() (lcdblib.snakemake.interface.SampleHandler method) fisher() (in module lcdblib.stats.fisher) fisher_tables() (in module lcdblib.stats.fisher) flatten() (in module lcdblib.utils.utils)

G

getLayers() (lcdblib.images.SVG.nb_svg method)

H

hisat2_index_from_prefix() (in module lcdblib.snakemake.aligners)

I

import_conversion() (in module lcdblib.utils.chrom_convert) InfoFilter (class in lcdblib.logger)

items() (lcdblib.parse.fastqc.FastQC method) (lcdblib.plotting.results_table.LazyDict method)

K

keys() (lcdblib.parse.fastqc.FastQC method) (lcdblib.plotting.results_table.LazyDict method)

L

LazyDict (class in lcdblib.plotting.results_table) lcdblib (module) lcdblib.expression (module) lcdblib.expression.expression_utils (module) lcdblib.images (module) lcdblib.images.SVG (module) lcdblib.logger (module) lcdblib.pandas (module) lcdblib.pandas.utils (module) lcdblib.parse (module) lcdblib.parse.atropos (module) lcdblib.parse.bamtools (module) lcdblib.parse.dupradar (module) lcdblib.parse.fastq_screen (module) lcdblib.parse.fastqc (module) lcdblib.parse.featurecounts (module) lcdblib.parse.picard (module) lcdblib.parse.rseqc (module) lcdblib.parse.samtools (module)

lcdblib.plotting (module) lcdblib.plotting.basic (module) lcdblib.plotting.colormap_adjust (module) lcdblib.plotting.compare_rnaseq_and_chipseq (module), [1] lcdblib.plotting.results_table (module) lcdblib.snakemake (module) lcdblib.snakemake.aligners (module) lcdblib.snakemake.helpers (module) lcdblib.snakemake.interface (module) lcdblib.stats (module) lcdblib.stats.fisher (module) lcdblib.utils (module) lcdblib.utils.chrom_convert (module) lcdblib.utils.imports (module) lcdblib.utils.utils (module) lfc_column (lcdblib.plotting.results_table.DESeq2Results attribute) (lcdblib.plotting.results_table.DifferentialExpressionResults attribute) (lcdblib.plotting.results_table.EdgeRResults attribute) limits (lcdblib.plotting.results_table.MarginalHistScatter attribute) lowerTriangle() (in module lcdblib.plotting.basic)

M

ma_plot() (lcdblib.plotting.results_table.DifferentialExpressionResults method) main() (in module lcdblib.utils.chrom_convert) make_input() (lcdblib.snakemake.interface.SampleHandler method) make_relative_symlink() (in module lcdblib.utils.utils)

maPlot() (in module lcdblib.plotting.basic) MarginalHistScatter (class in lcdblib.plotting.results_table) mean_column (lcdblib.plotting.results_table.DESeq2Results attribute) (lcdblib.plotting.results_table.DifferentialExpressionResults attribute) (lcdblib.plotting.results_table.EdgeRResults attribute)

N

nb_svg (class in lcdblib.images.SVG)

P

PairGrid (class in lcdblib.plotting.basic) parse_atropos() (in module lcdblib.parse.atropos) parse_bamStat() (in module lcdblib.parse.rseqc) parse_bamtools_stats() (in module lcdblib.parse.bamtools) parse_dupradar() (in module lcdblib.parse.dupradar) parse_fastqc() (in module lcdblib.parse.fastqc) parse_fastqc_adapter_content() (in module lcdblib.parse.fastqc) parse_fastqc_basic_stats() (in module lcdblib.parse.fastqc) parse_fastqc_kmer_content() (in module lcdblib.parse.fastqc) parse_fastqc_overrepresented_seq() (in module lcdblib.parse.fastqc) parse_fastqc_per_base_n_content() (in module lcdblib.parse.fastqc) parse_fastqc_per_base_seq_content() (in module lcdblib.parse.fastqc) parse_fastqc_per_base_seq_quality() (in module lcdblib.parse.fastqc) parse_fastqc_per_seq_gc_content() (in module lcdblib.parse.fastqc) parse_fastqc_per_seq_quality() (in module lcdblib.parse.fastqc) parse_fastqc_seq_dup_level() (in module lcdblib.parse.fastqc) parse_fastqc_sequence_length() (in module lcdblib.parse.fastqc) parse_featureCounts_counts() (in module lcdblib.parse.featurecounts) parse_featureCounts_summary() (in module lcdblib.parse.featurecounts)

parse_fqscreen() (in module lcdblib.parse.fastq_screen) parse_from_zip() (lcdblib.parse.fastqc.FastQC class method) parse_geneBodyCoverage() (in module lcdblib.parse.rseqc) parse_inferExperiment() (in module lcdblib.parse.rseqc) parse_picard_markduplicate_metrics() (in module lcdblib.parse.picard) parse_picardCollect_hist() (in module lcdblib.parse.picard) parse_picardCollect_summary() (in module lcdblib.parse.picard) parse_samtools_stats() (in module lcdblib.parse.samtools) parse_tin() (in module lcdblib.parse.rseqc) plot() (in module lcdblib.plotting.compare_rnaseq_and_chipseq), [1] prefix_from_bowtie2_index() (in module lcdblib.snakemake.aligners) prefix_from_hisat2_index() (in module lcdblib.snakemake.aligners) print_2x2_table() (in module lcdblib.stats.fisher) print_col_perc_table() (in module lcdblib.stats.fisher) print_row_perc_table() (in module lcdblib.stats.fisher) pval_column (lcdblib.plotting.results_table.DESeq2Results attribute) (lcdblib.plotting.results_table.DifferentialExpressionResults attribute) (lcdblib.plotting.results_table.EdgeRResults attribute) pybedtools_convert() (in module lcdblib.utils.chrom_convert) pysam_convert() (in module lcdblib.utils.chrom_convert)

R

radviz() (lcdblib.plotting.results_table.ResultsTable method) reindex_to() (lcdblib.plotting.results_table.ResultsTable method)

resolve_name() (in module lcdblib.utils.imports) ResultsTable (class in lcdblib.plotting.results_table) rscript() (in module lcdblib.snakemake.helpers)

S

SampleHandler (class in lcdblib.snakemake.interface) scatter() (lcdblib.plotting.results_table.ResultsTable method)

smart_colormap() (in module lcdblib.plotting.colormap_adjust) split_ranges() (in module lcdblib.parse.fastqc)

T

table_from_bool() (in module lcdblib.stats.fisher) temp_env() (in module lcdblib.utils.utils)

test_flatten() (in module lcdblib.utils.utils) tidy_dataframe() (in module lcdblib.pandas.utils)

U

unchanged() (lcdblib.plotting.results_table.DifferentialExpressionResults method) update() (lcdblib.plotting.results_table.ResultsTable method)

update_recursive() (in module lcdblib.utils.utils) updatecopy() (in module lcdblib.utils.utils) upregulated() (lcdblib.plotting.results_table.DifferentialExpressionResults method)

V

values() (lcdblib.parse.fastqc.FastQC method) (lcdblib.plotting.results_table.LazyDict method)

X

xmax (lcdblib.plotting.results_table.MarginalHistScatter attribute)

xmin (lcdblib.plotting.results_table.MarginalHistScatter attribute)

Y

ymax (lcdblib.plotting.results_table.MarginalHistScatter attribute)

ymin (lcdblib.plotting.results_table.MarginalHistScatter attribute)

Z

zFPKM() (in module lcdblib.expression.expression_utils)