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Fix Bioconductor submission issues and update vignette #2

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Fix Bioconductor submission issues and update vignette #2

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49b5f04
Fix R CMD check errors and warnings for Bioconductor submission
jpflores-13 Jun 17, 2026
0ecb846
Address BiocCheck notes and warnings for Bioconductor submission
Jun 17, 2026
646860b
Add Introduction section to vignette and fix CI dependency on loopcit…
Jul 9, 2026
b252df2
Fix pkgdown accessibility warnings and vignette title mismatch
Jul 9, 2026
fdc1731
Fix border adjustment bug in assignCommunities and update gitignore
Jul 13, 2026
527eb78
Fix border adjustment bugs, CI dependency resolution, and test setup
Jul 13, 2026
d4ac54a
Pre-install loopcityData from GitHub before dependency resolution
Jul 13, 2026
ce26123
Fix border adjustment logic in assignCommunities and add test
Jul 13, 2026
fc6c318
Add deterministic border-adjustment regression test and genome-wide d…
Jul 13, 2026
f109d30
Fix stale repo path in border_fix_genomewide_diff.R and ignore build …
jpflores-13 Jul 14, 2026
3905f5b
Add TAD null-model sparsity comparison for reviewer 2
jpflores-13 Jul 14, 2026
d44c94f
Ignore reviewer-response scratch files; fix zzz.R seqinfo bridge for …
jpflores-13 Jul 14, 2026
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -6,3 +6,4 @@
^docs$
^pkgdown$
^\.github$
^.*\.BiocCheck$
6 changes: 6 additions & 0 deletions .github/workflows/pkgdown.yaml
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Expand Up @@ -30,6 +30,12 @@ jobs:
with:
use-public-rspm: true

- name: Install loopcityData from GitHub
run: |
if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("jpflores-13/loopcityData")
shell: Rscript {0}

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::pkgdown, local::.
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9 changes: 9 additions & 0 deletions .gitignore
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Expand Up @@ -9,3 +9,12 @@ outputs/*
inst/doc
data/processed/
vignettes/*.png
*.BiocCheck/
*.tar.gz
*.Rcheck/
.batch_logs/

# Reviewer-response materials (BioC resubmission) — kept locally, not in the package
inst/scripts/tad_null_model_sparsity.R
figures/tad_null_model_sparsity.pdf
inst/scripts/call_tads_arrowhead.sbatch
14 changes: 10 additions & 4 deletions DESCRIPTION
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Expand Up @@ -2,9 +2,13 @@ Package: loopcity
Type: Package
Title: Call Chromatin Communities From Hi-C Data
Version: 0.1.0
Authors@R: person("Sarah", "Parker", role = c("aut", "cre"),
email = "smp3800@gmail.com",
comment = c(ORCID = "0000-0002-2700-3979"))
Authors@R: c(
person("Sarah", "Parker", role = c("aut", "cre"),
email = "smp3800@gmail.com",
comment = c(ORCID = "0000-0002-2700-3979")),
person("Howard Hughes Medical Institute", role = "fnd"),
person("National Institutes of Health", role = "fnd"),
person("National Science Foundation", role = "fnd"))
Description: Tools for assigning and visualizing chromatin community interactions from Hi-C data.
License: AGPL (>= 3)
Encoding: UTF-8
Expand Down Expand Up @@ -34,12 +38,14 @@ Imports:
stats,
S4Vectors
Depends:
R (>= 4.1.0)
R (>= 4.6.0)
biocViews: Software, HiC, Sequencing, Epigenetics, Network, Clustering,
Visualization
BugReports: https://github.com/sarmapar/loopcity/issues
URL:
https://sarmapar.com/loopcity/,
https://github.com/sarmapar/loopcity
VignetteBuilder: knitr
Config/Needs/website: github::jpflores-13/loopcityData
Config/roxygen2/version: 8.0.0
RoxygenNote: 7.3.2
4 changes: 4 additions & 0 deletions NEWS.md
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@@ -0,0 +1,4 @@
# loopcity 0.1.0

* Initial release. Tools for assigning and visualizing chromatin community
interactions from Hi-C data.
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