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Changelog

Source: NEWS.md

echoannot 1.0.1

Bug fixes

  • Remove XGR from Remotes to fix GHA dependency installation failure (dnet/supraHex unavailable on Bioconductor devel). XGR remains in Suggests with requireNamespace() guards.
  • Add "aut" role to maintainer in DESCRIPTION (required by --as-cran).

echoannot 1.0.0

New features

  • Remove deprecated NOTT2019_plot_bp_query and NOTT2019_epigenomic_histograms wrappers.

Bug fixes

  • Move XGR from Imports to Suggests with requireNamespace() guards, since XGR is no longer maintained on CRAN/Bioconductor.
  • Update R requirement from >= 4.0.0 to >= 4.1.
  • Rd: convert \itemize to \describe for named lists, add \dontrun{} guards to examples requiring XGR.
  • Remove tracked .DS_Store files.

echoannot 0.99.13

Bug fixes

  • Local R CMD check fixes and compatibility updates.

echoannot 0.99.12

New features

  • Standardize rworkflows.yml with canonical template: enable Docker on ghcr.io, set write-all permissions.
  • Move XGR from Imports to Suggests with requireNamespace() guards.
  • Update R requirement from >= 4.0.0 to >= 4.1.
  • Fix .gitignore patterns for .tbi and Rplots.pdf files.
  • Remove tracked .DS_Store files.

echoannot 0.99.11

New features

  • Implement rworkflows

echoannot 0.99.10

New features

  • annotation_file_name:
    • New export function.
  • ROADMAP_merge_and_process_grl –> ROADMAP_merge_and_process
  • ROADMAP_query:
    • Embed ROADMAP_merge_and_process as an option.
    • Make save_path more unique by adding params to name.
  • ROADMAP_tabix:
    • Can now find a read in existing files of the same.
  • XGR_query –> XGR_query:
    • Embed n_top as an option, passed to XGR_filter_assays and XGR_filter_sources.
  • xgr_query –> xgr_example (to avoid conflict with func name)
  • Move functions to echoplot:
    • ROADMAP_plot and plotting subfunctions.
    • XGR_plot and plotting subfunctions.
  • Move functions to downloadR:
    • zenodo_upload
    • zenodo_list
  • Remove Imports:
    • scales
    • piggyback
    • RColorBrewer
    • zen4R
  • test_enrichment:
    • Can convert data.tables to GRL too.
    • Pass up args from PermTest: min.parallel,force.parallel
    • Allow users to set seed.
  • Move zenodo_list to downloadR

Bug fixes

  • ROADMAP_query: rtracklayer::import has some bugs that prevent it from importing certain bed.gz files. So implemented a workaround using custom functions instead.
  • Reduce vignette sizes to <5Mb.
  • Fix super_summary_plot unit tests.
  • Switch website to gh-pages branch.
  • Fix GHA: @master –> @v2
  • NOTT2019_plac_seq_plot:
    • Get rid of hjust warning.

echoannot 0.99.9

New features

  • Added MOTIFBREAKR suite of functions.
    • MOTIFBREAKR,MOTIFBREAKR_calc_pvals,MOTIFBREAKR_filter, MOTIFBREAKR_plot,MOTIFBREAKR_summarize
    • Fully documented.
    • First attempts to get parallelization working.
    • Passes up other args from motifbreakR core functions.
    • Saves motif plots as PDFs.
  • Added get_bpparam function.
  • Added filter_chromatin_states function (internal).
  • Move to echodata package:
    • get_SNPgroup_counts
    • results_report
    • merge_finemapping_results: and split annotation portions into new annotate_snps.

Bug fixes

  • get_SNPgroup_counts:
    • Get rid of .dots and .groups warnings.
  • Update main vignette to reflect all changes.
  • annotate_snps: Fix subfunctions (there’s been some updates to tool outputs).
  • Fix ROADMAP_query.

echoannot 0.99.8

New features

  • Split peakyfinders from echoannot.
  • cell_type_specifity: Derive a EWCE-inspired specificity score for each cell-type and show in plot.

Bug fixes

  • merged_finemap_results: Fix overwriting multifinemap_pattern.

echoannot 0.99.7

New features

  • import_peaks_geo:
    • Can now import/call peaks in parallel, by splitting queries across chromosomes.
    • Can now import >1 peak type at a time, and documents it in “peaktype” col. 
  • import_peaks:
    • Pass up args: regex_queries, split_chromosomes
  • New function: process_ids:
    • Able to get GSM sample names from GSE project ID.
  • Split import_peaks_geo into separateimport_peaks_* functions for each file type.

Bug fixes

  • When only one peak type is returned from GEO search, prevent mapply from turning the results into a matrix with SIMPLIFY=FALSE.
  • Return empty GenomicRanges::GRanges() instead of error/NA/NULL during errors, so you can still merge at the end.

echoannot 0.99.6

New features

  • XGR_query: Set dat=NULL to return genome-wide data.
  • New vignette: cell_type_specific_epigenomics, with Nott2019 and Corces2020 data.

Bug fixes

  • prepare_highlight_plac_data: Allow to plot overlap with any SNP group (not just consensus SNPs).

echoannot 0.99.5

New features

  • Moved get_CS_counts/get_CS_bins to echodata.
  • Cache remote data resources in echoannot-specific folder.
  • Add XGR GitHub installation again (CRAN installation not working again?).
  • Shorten Nott2019 ref links.
  • Pass all CRAN checks.

Bug fixes

  • Added R.utils/tools to Imports.
  • Added GEOquery/regioneR/ BSgenome.Hsapiens.UCSC.hg38/BSgenome.Hsapiens.UCSC.hg19 to Suggests.
  • Updated GHA workflow to account for git security changes.
  • Fixed convert_plots when converting Tracks to list of ggplots.
  • Fixed merge_celltype_specific_epigenomics
    • Added caching mechanism.
  • Use echodata::<locus> data instead of portal data for Getting started vignette.
  • Replace file.path with paste.
  • Replace “echoR” with “echoR_mini”.
  • Set timeout with multiple approaches: options,httr::timeout, httr::config.

echoannot 0.99.4

New features

  • New functions
    • import_peaks: Search for peak files in GEO/ENCODE, or compute them from bedGraph files.
    • call_peaks: Call peaks from bedGraph files using MACSr.
    • test_enrichment: Run permutation enrichment tests.

echoannot 0.99.3

Bug fixes

  • Update to match latest echotabix changes.
  • Update GHA workflow.

echoannot 0.99.3

New features

  • Added function convert_plots.

Bug fixes

  • Move as many Imports to Suggests as possible.
  • GHA servers can’t install XGR from CRAN. Switching to GitHub remote installation until they fix this.
  • Removed docs/ folder.
  • Reduced vignette size.
  • Transition all usage of ggplot2 to requireNamespace method to reduce NAMESPACE.
  • Make all new col assignments in GRanges objects use the proper mcols syntax.
  • Make sure all GRanges in UCSC format in NOTT2019_plac_seq_plot.
  • Subdivide NOTT2019_plac_seq_plot into subfunctions.
  • New exports:
    • NOTT2019_get_epigenomic_peaks

echoannot 0.99.2

New features

  • Added a NEWS.md file to track changes to the package.
  • Replace the following with echoverseTemplate versions:
    • New hex logo.
    • GHA
    • README
    • Vignette header
  • Offload functions to echodata:
    • assign_lead_snp
    • find_consensus_snps
    • update_cols
    • biomart_geneInfo
    • find_top_consensus
    • dt_to_granges
    • is_granges
    • granges_to_bed
    • reassign_lead_snps
  • Renamed all functions to exclude “.”:
    • “ROADMAP.” –> “ROADMAP_”
    • “NOTT_2019.” –> “NOTT2019_”
    • etc.
  • Added xgr_example example data.
  • Added unit tests for super_summary_plot and its subfunctions.
  • Offloaded all liftover functions to echotabix
  • Made new wrapper functions to simplify importing/plotting pipelines:
    • XGR_plot
    • ROADMAP_plot