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Attempt using plyxp for some cases in tidySummarizedExperiment

Status: Open.

#19 In tidyomics/genomics-todos;

· mikelove opened on Jun 26, 2025

DESeq2 workflow (rnaseqGene) using tidybulk

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#18 In tidyomics/genomics-todos;

· mikelove opened on May 12, 2025

LD score regression (LDSC) and R/tidyomics intergration

enhancementNew feature or requestNew feature or request

Status: Open.

#17 In tidyomics/genomics-todos;

· mikelove opened on Apr 3, 2025

<code>biocmask</code>: data masks for S4 objects, especially SummarizedExperiment

enhancementNew feature or requestNew feature or request

Status: Open.

#16 In tidyomics/genomics-todos;

· mikelove opened on Sep 4, 2024

tidyomics project-wide challenge: add more cross-package tutorials

Status: Open.

#14 In tidyomics/genomics-todos;

· mikelove opened on Feb 15, 2024

Example of scATAC-seq pseudobulk analysis for differential accessibility testing

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#11 In tidyomics/genomics-todos;

· jeremymsimon opened on Oct 26, 2023

<code>plyranges</code>: facilitate adding metadata columns via <code>join_mcols_*</code>

enhancementNew feature or requestNew feature or request

Status: Open.

#10 In tidyomics/genomics-todos;

· mikelove opened on Sep 23, 2023

use <code>pillar</code> to add aesthetics to the columns of the <code>tibble</code> interface of <code>tidySCE</code>, <code>tidyseurat</code>, <code>tidySE</code>

enhancementNew feature or requestNew feature or request

Status: Open.

#9 In tidyomics/genomics-todos;

· stemangiola opened on Aug 25, 2023

Write/teach workshop on bootRanges

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#7 In tidyomics/genomics-todos;

· mikelove opened on Aug 21, 2023

modernize tidy transcriptomics and genomics with dplyr &gt; 1.0.0 and new tidyr

enhancementNew feature or requestNew feature or request

Status: Open.

#6 In tidyomics/genomics-todos;

· stemangiola opened on Aug 15, 2023

Example of ATAC-seq processing combining plyranges and tidybulk/tidySummarizedExperiment

documentationImprovements or additions to documentationImprovements or additions to documentation

good first issueGood for newcomersGood for newcomers

Status: Open.

#1 In tidyomics/genomics-todos;

· mikelove opened on Aug 15, 2023

<code>plyranges</code>: <code>join_overlap</code> but also include distance column

enhancementNew feature or requestNew feature or request

Status: Open.

#2 In tidyomics/genomics-todos;

· mikelove opened on Aug 3, 2023