Package: plyranges 1.27.0
Michael Love
plyranges: A fluent interface for manipulating GenomicRanges
A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.
Authors:
plyranges_1.27.0.tar.gz
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plyranges.pdf |plyranges.html✨
plyranges/json (API)
NEWS
| # Install 'plyranges' in R: |
| install.packages('plyranges', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tidyomics/plyranges/issues
On BioConductor:plyranges-1.27.0(bioc 3.21)plyranges-1.26.0(bioc 3.20)
infrastructuredatarepresentationworkflowstepcoveragebioconductordata-analysisdplyrgenomic-rangesgenomicstidy-data
Last updated 21 days agofrom:b1cbb5d2ca. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 08 2024 |
| R-4.5-win | WARNING | Nov 08 2024 |
| R-4.5-linux | WARNING | Nov 08 2024 |
| R-4.4-win | WARNING | Nov 08 2024 |
| R-4.4-mac | ERROR | Nov 08 2024 |
| R-4.3-win | WARNING | Nov 08 2024 |
| R-4.3-mac | ERROR | Nov 08 2024 |
Exports:!!!!!%>%%intersect%%setdiff%%union%add_nearest_distanceadd_nearest_distance_downstreamadd_nearest_distance_leftadd_nearest_distance_rightadd_nearest_distance_upstreamanchoranchor_3panchor_5panchor_centeranchor_centreanchor_endanchor_startarrangeas_grangesas_irangesas_rangesbetweenbind_rangeschop_by_gapschop_by_intronscomplement_rangescomplement_ranges_directedcompute_coveragecount_overlapscount_overlaps_directedcount_overlaps_withincount_overlaps_within_directeddisjoin_rangesdisjoin_ranges_directedexpand_rangesfilterfilter_by_non_overlapsfilter_by_non_overlaps_directedfilter_by_overlapsfilter_by_overlaps_directedfind_overlapsfind_overlaps_directedfind_overlaps_withinfind_overlaps_within_directedflank_downstreamflank_leftflank_rightflank_upstreamgenome_infoget_genome_infogroup_bygroup_by_overlapsgroup_varsgroupsid_to_columnintersect_rangesintersect_ranges_directedinterweavejoin_followjoin_follow_leftjoin_follow_upstreamjoin_nearestjoin_nearest_downstreamjoin_nearest_leftjoin_nearest_rightjoin_nearest_upstreamjoin_overlap_innerjoin_overlap_inner_directedjoin_overlap_inner_withinjoin_overlap_inner_within_directedjoin_overlap_intersectjoin_overlap_intersect_directedjoin_overlap_intersect_withinjoin_overlap_intersect_within_directedjoin_overlap_leftjoin_overlap_left_directedjoin_overlap_left_withinjoin_overlap_left_within_directedjoin_overlap_selfjoin_overlap_self_directedjoin_overlap_self_withinjoin_overlap_self_within_directedjoin_precedejoin_precede_downstreamjoin_precede_rightmutatenn_distinctnames_to_columnoverscope_rangespair_followpair_nearestpair_overlapspair_precederead_bamread_bedread_bed_graphread_bigwigread_gffread_gff1read_gff2read_gff3read_narrowpeaksread_wigreduce_rangesreduce_ranges_directedremove_namesselectset_endset_genome_infoset_seqnamesset_startset_strandset_widthsetdiff_rangessetdiff_ranges_directedshift_downstreamshift_leftshift_rightshift_upstreamsliceslide_rangesspanstretchsummarisesummarizetile_rangesunanchorungroupunion_rangesunion_ranges_directedwrite_bedwrite_bed_graphwrite_bigwigwrite_gffwrite_gff1write_gff2write_gff3write_narrowpeakswrite_wig
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| plyranges: a grammar of genomic data manipulation | plyranges-package plyranges |
| Row-wise set operations on Ranges objects | %intersect% %setdiff% %union% between span |
| Add distance to nearest neighbours between two Ranges objects | add_nearest_distance add_nearest_distance_downstream add_nearest_distance_left add_nearest_distance_right add_nearest_distance_upstream |
| Anchored Ranges objects | anchor anchor_3p anchor_5p anchor_center anchor_centre anchor_end anchor_start unanchor |
| Sort a Ranges object | arrange.Ranges |
| Construct a I/GRanges object from a tibble or data.frame | as_granges as_iranges |
| Coerce an Rle or RleList object to Ranges | as_ranges |
| Combine Ranges by concatentating them together | bind_ranges |
| Group a GRanges object by introns or gaps | chop_by_gaps chop_by_introns |
| Compute coverage over a Ranges object | compute_coverage |
| Count the number of overlaps between two Ranges objects | count_overlaps count_overlaps.GenomicRanges count_overlaps.IntegerRanges count_overlaps_directed count_overlaps_directed.GenomicRanges count_overlaps_within count_overlaps_within.GenomicRanges count_overlaps_within.IntegerRanges count_overlaps_within_directed count_overlaps_within_directed.GenomicRanges |
| DeferredGenomiRanges objects | DeferredGenomicRanges-class |
| Disjoin then aggregate a Ranges object | disjoin_ranges disjoin_ranges_directed |
| Expand list-columns in a Ranges object | expand_ranges |
| An abstract class to represent operations performed over a file | BamFileOperator-class FileOperator-class |
| Filter by overlapping/non-overlapping ranges | filter_by_non_overlaps filter_by_non_overlaps_directed filter_by_overlaps filter_by_overlaps_directed |
| Subset a 'Ranges' object | filter-ranges filter.Ranges |
| Find overlap between two Ranges | find_overlaps find_overlaps.GenomicRanges find_overlaps.IntegerRanges find_overlaps_directed find_overlaps_directed.GenomicRanges find_overlaps_within find_overlaps_within.GenomicRanges find_overlaps_within.IntegerRanges find_overlaps_within_directed find_overlaps_within_directed.GenomicRanges group_by_overlaps group_by_overlaps.GenomicRanges group_by_overlaps.IntegerRanges |
| Generate flanking regions | flank_downstream flank_left flank_right flank_upstream |
| Group a Ranges by one or more variables | GroupedGenomicRanges-class GroupedIntegerRanges-class groups.GroupedGenomicRanges groups.GroupedIntegerRanges group_by-ranges group_by.GenomicRanges ungroup.GroupedGenomicRanges |
| Vector-wise Range set-operations | complement_ranges complement_ranges_directed intersect_ranges intersect_ranges_directed setdiff_ranges setdiff_ranges_directed union_ranges union_ranges_directed |
| Interweave a pair of Ranges objects together | interweave |
| Find following Ranges | join_follow join_follow_left join_follow_upstream |
| Find nearest neighbours between two Ranges objects | join_nearest join_nearest_downstream join_nearest_left join_nearest_right join_nearest_upstream |
| Join by overlapping Ranges | join_overlap_inner join_overlap_inner_directed join_overlap_inner_within join_overlap_inner_within_directed join_overlap_intersect join_overlap_intersect_directed join_overlap_intersect_within join_overlap_intersect_within_directed join_overlap_left join_overlap_left_directed join_overlap_left_within join_overlap_left_within_directed |
| Find overlaps within a Ranges object | join_overlap_self join_overlap_self_directed join_overlap_self_within join_overlap_self_within_directed |
| Find preceding Ranges | join_precede join_precede_downstream join_precede_right |
| Modify a Ranges object | mutate.Ranges |
| Compute the number of ranges in each group. | n |
| Compute the number of distinct unique values in a vector or List | n_distinct |
| Create an overscoped environment from a Ranges object | overscope_ranges |
| Pair together two ranges objects | pair_follow pair_nearest pair_overlaps pair_precede |
| Construct annotation information | genome_info get_genome_info ranges-info set_genome_info |
| Read a BAM file | read_bam |
| Read a BED or BEDGraph file | read_bed read_bed_graph read_narrowpeaks |
| Read a BigWig file | read_bigwig |
| Read a GFF/GTF/GVT file | read_gff read_gff1 read_gff2 read_gff3 |
| Read a WIG file | read_wig |
| Reduce then aggregate a Ranges object | reduce_ranges reduce_ranges_directed |
| Tools for working with named Ranges | id_to_column names_to_column remove_names |
| Select metadata columns of the Ranges object by name or position | select.Ranges |
| Functional setters for Ranges objects | set_end set_seqnames set_start set_strand set_width |
| Shift all coordinates in a genomic interval left or right, upstream or downstream | shift_downstream shift_left shift_right shift_upstream |
| Choose rows by their position | slice.GroupedGenomicRanges slice.GroupedIntegerRanges slice.Ranges |
| Stretch a genomic interval | stretch |
| Reduce multiple values in a Ranges down to a single value | summarise.Ranges |
| Slide or tile over a Ranges object | slide_ranges tile_ranges |
| Write a BED or BEDGraph file | write_bed write_bed_graph write_narrowpeaks |
| Write a BigWig file | write_bigwig |
| Write a GFF(123) file | write_gff write_gff1 write_gff2 write_gff3 |
| Write a WIG file | write_wig |
