A fluent interface for manipulating GenomicRanges

Global functions | |
---|---|

!! | Man page |

!!! | Man page |

%>% | Man page |

%intersect% | Man page |

%setdiff% | Man page |

%union% | Man page |

BamFileOperator-class | Man page |

DeferredGenomicRanges-class | Man page |

FileOperator-class | Man page |

GroupedGenomicRanges-class | Man page |

GroupedIntegerRanges-class | Man page |

add_na_seqlevels | Source code |

all_genomic_ranges | Source code |

all_integer_ranges | Source code |

anchor | Man page Source code |

anchor.AnchoredGenomicRanges | Source code |

anchor_3p | Man page Source code |

anchor_3p.GenomicRanges | Source code |

anchor_5p | Man page Source code |

anchor_5p.GenomicRanges | Source code |

anchor_center | Man page Source code |

anchor_center.GenomicRanges | Source code |

anchor_center.IntegerRanges | Source code |

anchor_centre | Man page Source code |

anchor_end | Man page Source code |

anchor_end.GenomicRanges | Source code |

anchor_end.IntegerRanges | Source code |

anchor_start | Man page Source code |

anchor_start.GenomicRanges | Source code |

anchor_start.IntegerRanges | Source code |

arrange | Man page |

arrange.DelegatingGenomicRanges | Source code |

arrange.Ranges | Man page Source code |

as_granges | Man page Source code |

as_granges.data.frame | Source code |

as_granges.default | Source code |

as_iranges | Man page Source code |

as_iranges.data.frame | Source code |

as_iranges.default | Source code |

as_ranges | Man page Source code |

as_ranges.Rle | Source code |

as_ranges.RleList | Source code |

between | Man page Source code |

bind_ranges | Man page Source code |

bind_rng | Source code |

bioc_generics | Source code |

check_id_var | Source code |

check_names | Source code |

check_which_label | Source code |

chop_by_gaps | Man page Source code |

chop_by_gaps.DeferredGenomicRanges | Source code |

chop_by_gaps.GenomicRanges | Source code |

chop_by_introns | Man page Source code |

chop_by_introns.DeferredGenomicRanges | Source code |

chop_by_introns.GenomicRanges | Source code |

complement_ranges | Man page Source code |

complement_ranges.GenomicRanges | Source code |

complement_ranges.IntegerRanges | Source code |

complement_ranges_directed | Man page Source code |

complement_ranges_directed.GenomicRanges | Source code |

compute_coverage | Man page Source code |

compute_coverage.default | Source code |

count_overlaps | Man page Source code |

count_overlaps.GenomicRanges | Man page Source code |

count_overlaps.IntegerRanges | Man page Source code |

count_overlaps_directed | Man page Source code |

count_overlaps_directed.GenomicRanges | Man page Source code |

count_overlaps_within | Man page Source code |

count_overlaps_within.GenomicRanges | Man page Source code |

count_overlaps_within.IntegerRanges | Man page Source code |

count_overlaps_within_directed | Man page Source code |

count_overlaps_within_directed.GenomicRanges | Man page Source code |

disjoin_ranges | Man page Source code |

disjoin_ranges.GenomicRanges | Source code |

disjoin_ranges.GroupedGenomicRanges | Source code |

disjoin_ranges.GroupedIntegerRanges | Source code |

disjoin_ranges.IntegerRanges | Source code |

disjoin_ranges_directed | Man page Source code |

disjoin_ranges_directed.GenomicRanges | Source code |

disjoin_ranges_directed.GroupedGenomicRanges | Source code |

expand_by_hits | Source code |

expand_rng_by_cigar | Source code |

filter | Man page |

filter-ranges | Man page |

filter.BamFileOperator | Source code |

filter.DeferredGenomicRanges | Source code |

filter.DelegatingGenomicRanges | Source code |

filter.GroupedGenomicRanges | Source code |

filter.Ranges | Man page Source code |

filter_by_non_overlaps | Man page Source code |

filter_by_non_overlaps.GenomicRanges | Source code |

filter_by_non_overlaps.IntegerRanges | Source code |

filter_by_overlaps | Man page Source code |

filter_by_overlaps.BamFileOperator | Source code |

filter_by_overlaps.DeferredGenomicRanges | Source code |

filter_by_overlaps.GenomicRanges | Source code |

filter_by_overlaps.IntegerRanges | Source code |

filter_grp | Source code |

filter_rng | Source code |

find_overlaps | Man page Source code Source code |

find_overlaps.GenomicRanges | Man page Source code |

find_overlaps.IntegerRanges | Man page Source code |

find_overlaps_directed | Man page Source code |

find_overlaps_directed.GenomicRanges | Man page Source code |

find_overlaps_within | Man page Source code |

find_overlaps_within.GenomicRanges | Man page Source code |

find_overlaps_within.IntegerRanges | Man page Source code |

find_overlaps_within_directed | Man page Source code |

find_overlaps_within_directed.GenomicRanges | Man page Source code |

flank_downstream | Man page Source code |

flank_left | Man page Source code |

flank_right | Man page Source code |

flank_upstream | Man page Source code |

galn_to_grng | Source code |

genome_info | Man page Source code |

get_genome_info | Man page Source code |

get_genome_info.BamFileOperator | Source code |

get_genome_info.DeferredGenomicRanges | Source code |

get_genome_info.Seqinfo | Source code |

get_genome_info.default | Source code |

grng_construct | Source code |

group_by | Man page |

group_by-ranges | Man page |

group_by.DeferredGenomicRanges | Source code |

group_by.GenomicRanges | Man page Source code |

group_by.IntegerRanges | Source code |

group_by_overlaps | Man page Source code |

group_by_overlaps.GenomicRanges | Man page Source code |

group_by_overlaps.IntegerRanges | Man page Source code |

group_vars | Man page |

group_vars.GroupedGenomicRanges | Source code |

group_vars.Ranges | Source code |

groups | Man page |

groups.GroupedGenomicRanges | Man page Source code |

groups.GroupedIntegerRanges | Man page |

groups.Ranges | Source code |

initialize_AnchoredRanges | Source code |

initialize_GroupedRanges | Source code |

intersect_ranges | Man page Source code |

intersect_ranges.GenomicRanges | Source code |

intersect_ranges.IntegerRanges | Source code |

intersect_ranges_directed | Man page Source code |

intersect_ranges_directed.GenomicRanges | Source code |

interweave | Man page Source code |

irng_construct | Source code |

is_empty_delegate | Source code |

is_empty_quos | Source code |

join_follow | Man page Source code |

join_follow.GenomicRanges | Source code |

join_follow.IntegerRanges | Source code |

join_follow_left | Man page Source code |

join_follow_left.GenomicRanges | Source code |

join_follow_left.IntegerRanges | Source code |

join_follow_upstream | Man page Source code |

join_follow_upstream.GenomicRanges | Source code |

join_intersect | Source code |

join_nearest | Man page Source code |

join_nearest.GenomicRanges | Source code |

join_nearest.IntegerRanges | Source code |

join_nearest_downstream | Man page Source code |

join_nearest_downstream.GenomicRanges | Source code |

join_nearest_left | Man page Source code |

join_nearest_left.GenomicRanges | Source code |

join_nearest_left.IntegerRanges | Source code |

join_nearest_right | Man page Source code |

join_nearest_right.GenomicRanges | Source code |

join_nearest_right.IntegerRanges | Source code |

join_nearest_upstream | Man page Source code |

join_nearest_upstream.GenomicRanges | Source code |

join_overlap_inner | Man page Source code |

join_overlap_inner_directed | Man page Source code |

join_overlap_inner_within | Man page Source code |

join_overlap_inner_within_directed | Man page Source code |

join_overlap_intersect | Man page Source code |

join_overlap_intersect.GenomicRanges | Source code |

join_overlap_intersect.IntegerRanges | Source code |

join_overlap_intersect_directed | Man page Source code |

join_overlap_intersect_directed.GenomicRanges | Source code |

join_overlap_intersect_within | Man page Source code |

join_overlap_intersect_within.GenomicRanges | Source code |

join_overlap_intersect_within.IntegerRanges | Source code |

join_overlap_intersect_within_directed | Man page Source code |

join_overlap_intersect_within_directed.GenomicRanges | Source code |

join_overlap_left | Man page Source code Source code |

join_overlap_left.GenomicRanges | Source code |

join_overlap_left.IntegerRanges | Source code |

join_overlap_left_directed | Man page Source code |

join_overlap_left_directed.GenomicRanges | Source code |

join_overlap_left_within | Man page Source code |

join_overlap_left_within.GenomicRanges | Source code |

join_overlap_left_within.IntegerRanges | Source code |

join_overlap_left_within_directed | Man page Source code |

join_overlap_left_within_directed.GenomicRanges | Source code |

join_overlap_self | Man page Source code |

join_overlap_self.GenomicRanges | Source code |

join_overlap_self_directed | Man page Source code |

join_overlap_self_directed.GenomicRanges | Source code |

join_overlap_self_within | Man page Source code |

join_overlap_self_within.GenomicRanges | Source code |

join_overlap_self_within_directed | Man page Source code |

join_overlap_self_within_directed.GenomicRanges | Source code |

join_precede | Man page Source code |

join_precede.GenomicRanges | Source code |

join_precede.IntegerRanges | Source code |

join_precede_downstream | Man page Source code |

join_precede_downstream.GenomicRanges | Source code |

join_precede_right | Man page Source code |

join_precede_right.GenomicRanges | Source code |

join_precede_right.IntegerRanges | Source code |

load_delegate | Source code |

load_genomic_file | Source code |

load_genomic_file.BamFileOperator | Source code |

make_group_inx | Source code |

make_hits | Source code |

make_mcols | Source code |

mcols_overlaps_update | Source code |

mutate | Man page |

mutate.DeferredGenomicRanges | Source code |

mutate.DelegatingGenomicRanges | Source code |

mutate.GroupedGenomicRanges | Source code |

mutate.Ranges | Man page Source code |

mutate_core | Source code |

mutate_grp | Source code |

mutate_mcols | Source code |

mutate_rng | Source code |

n | Man page Source code |

n_distinct | Man page Source code |

na_cols | Source code |

na_ranges | Source code |

new_DeferredGenomicRanges | Source code |

new_anchored_gr | Source code |

new_anchored_ir | Source code |

new_bam_ops | Source code |

new_grouped_gr | Source code |

new_grouped_ir | Source code |

norm_args_reader | Source code |

norm_args_reader_gff | Source code |

overscope_eval_update | Source code |

overscope_ranges | Man page Source code |

overscope_ranges.DelegatingGenomicRanges | Source code |

overscope_ranges.GroupedGenomicRanges | Source code |

overscope_ranges.Ranges | Source code |

pair_follow | Man page Source code |

pair_follow.GenomicRanges | Source code |

pair_follow.IntegerRanges | Source code |

pair_nearest | Man page Source code |

pair_nearest.GenomicRanges | Source code |

pair_nearest.IntegerRanges | Source code |

pair_overlaps | Man page Source code |

pair_overlaps.GenomicRanges | Source code |

pair_overlaps.IntegerRanges | Source code |

pair_precede | Man page Source code |

pair_precede.GenomicRanges | Source code |

pair_precede.IntegerRanges | Source code |

paired_alignments | Source code |

partition_rng | Source code |

plyranges | Man page |

plyranges-package | Man page |

quo_set_generic | Source code |

quos_set_env | Source code |

ranges-info | Man page |

ranges_vars | Source code |

read_bam | Man page Source code |

read_bed | Man page Source code |

read_bed_graph | Man page Source code |

read_bigwig | Man page Source code |

read_gff | Man page Source code |

read_gff1 | Man page Source code |

read_gff2 | Man page Source code |

read_gff3 | Man page Source code |

read_narrowpeaks | Man page Source code |

read_wig | Man page Source code |

reduce_by_grp | Source code |

reduce_ranges | Man page Source code |

reduce_ranges.GenomicRanges | Source code |

reduce_ranges.GroupedGenomicRanges | Source code |

reduce_ranges.GroupedIntegerRanges | Source code |

reduce_ranges.IntegerRanges | Source code |

reduce_ranges_directed | Man page Source code |

reduce_ranges_directed.GenomicRanges | Source code |

reduce_ranges_directed.GroupedGenomicRanges | Source code |

reduce_rng | Source code |

reduce_single | Source code |

reexports | Man page |

resize_by_strand | Source code |

rng_arrange | Source code |

scope_plyranges | Source code |

select | Man page |

select.BamFileOperator | Source code |

select.DeferredGenomicRanges | Source code |

select.DelegatingGenomicRanges | Source code |

select.Ranges | Man page Source code |

select_rng | Source code |

set_dots_named | Source code |

set_dots_unnamed | Source code |

set_end | Man page Source code |

set_end.Ranges | Source code |

set_genome_info | Man page Source code |

set_id_var | Source code |

set_seqnames | Man page Source code |

set_seqnames.GenomicRanges | Source code |

set_start | Man page Source code |

set_start.Ranges | Source code |

set_strand | Man page Source code |

set_strand.GenomicRanges | Source code |

set_width | Man page Source code |

set_width.AnchoredGenomicRanges | Source code |

set_width.AnchoredIntegerRanges | Source code |

set_width.Ranges | Source code |

setdiff_ranges | Man page Source code |

setdiff_ranges.GenomicRanges | Source code |

setdiff_ranges.IntegerRanges | Source code |

setdiff_ranges_directed | Man page Source code |

setdiff_ranges_directed.GenomicRanges | Source code |

shift_downstream | Man page Source code |

shift_left | Man page Source code |

shift_right | Man page Source code |

shift_upstream | Man page Source code |

show_AnchoredRanges | Source code |

show_GroupedRanges | Source code |

slide_ranges | Man page Source code |

slide_ranges.Ranges | Source code |

span | Man page Source code |

stretch | Man page Source code |

stretch.AnchoredGenomicRanges | Source code |

stretch.AnchoredIntegerRanges | Source code |

stretch.Ranges | Source code |

stretch_by_strand | Source code |

stretch_center | Source code |

summarise | Man page |

summarise.DeferredGenomicRanges | Source code |

summarise.DelegatingGenomicRanges | Source code |

summarise.DelegatingIntegerRanges | Source code |

summarise.GroupedGenomicRanges | Source code |

summarise.Ranges | Man page Source code |

summarize | Man page |

summarize_rng | Source code |

tbl_vars.GenomicRanges | Source code |

tidyverse-reexports | Man page |

tile_ranges | Man page Source code |

tile_ranges.Ranges | Source code |

unanchor | Man page Source code |

unanchor.AnchoredGenomicRanges | Source code |

ungroup | Man page |

ungroup.GroupedGenomicRanges | Man page Source code |

ungroup.Ranges | Source code |

union_ranges | Man page Source code |

union_ranges.GenomicRanges | Source code |

union_ranges.IntegerRanges | Source code |

union_ranges_directed | Man page Source code |

union_ranges_directed.GenomicRanges | Source code |

unnest | Man page |

unnest.GenomicRanges | Man page Source code |

unpaired_alignments | Source code |

validAnchoredRanges | Source code |

validGroupedRanges | Source code |

valid_flag_filters | Source code |

write_bed | Man page Source code |

write_bed_graph | Man page Source code |

write_bigwig | Man page Source code |

write_gff | Man page Source code |

write_gff1 | Man page Source code |

write_gff2 | Man page Source code |

write_gff3 | Man page Source code |

write_narrowpeaks | Man page Source code |

write_wig | Man page Source code |

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