Files in AlexsLemonade/scpcaTools
Single cell data tools for ScPCA
.Rbuildignore
.Rprofile
.dockerignore
.github/.gitignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/ISSUE_TEMPLATE/release-checklist.md
.github/workflows/R-CMD-check-current.yaml
.github/workflows/R-CMD-check-renv.yaml
.github/workflows/build-docker.yaml
.github/workflows/pr-commands.yaml
.gitignore
.lintr
.pre-commit-config.yaml
CONTRIBUTING.md
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/add_cell_mito_qc.R
R/add_cellhash_calls.R
R/add_gene_symbols.R
R/add_miQC.R
R/add_sample_metadata.R
R/add_vireo_calls.R
R/build_sce.R
R/calculate_ilisi.R
R/calculate_silhouette_width.R
R/calculate_within_batch_ari.R
R/cluster_sce.R
R/collapse_intron_counts.R
R/filter_counts.R
R/generate_qc_report.R
R/import_quant_data.R
R/integrate_sces.R
R/merge_altexp.R
R/merge_sce_list.R
R/metadata_to_coldata.R
R/processing_pcs.R
R/read_alevin.R
R/read_cellranger.R
R/read_kallisto.R
R/sce_to_anndata.R
R/sce_to_df.R
R/sce_to_seurat.R
R/scpcaTools-package.R
R/sim_sce.R
README.md
docker/README.md
docker/dependencies.R
docker/environment.yml
docker/make-requirements.sh
docker/renv_reports.lock
docker/renv_seurat.lock
docker/renv_slim.lock
docker/renv_zellkonverter.lock
docker/requirements.in
docker/requirements.txt
docker/requirements_anndata.in
docker/requirements_anndata.txt
docker/requirements_scvi.in
docker/requirements_scvi.txt
docker/scripts/install_scpca_deps.sh
docker/scripts/make-lockfile.R
inst/WORDLIST
inst/rmd/cite_qc.rmd
inst/rmd/multiplex_qc.rmd
inst/rmd/qc_report.rmd
inst/rmd/umap_qc.rmd
man/add_cell_mito_qc.Rd
man/add_cellhash_ids.Rd
man/add_demux_hashedDrops.Rd
man/add_demux_seurat.Rd
man/add_demux_vireo.Rd
man/add_gene_symbols.Rd
man/add_miQC.Rd
man/add_sample_metadata.Rd
man/build_sce.Rd
man/calculate_ilisi.Rd
man/calculate_silhouette_width.Rd
man/calculate_within_batch_ari.Rd
man/check_metadata.Rd
man/cluster_sce.Rd
man/coldata_to_df.Rd
man/collapse_intron_counts.Rd
man/downsample_pcs.Rd
man/filter_counts.Rd
man/filter_pcs.Rd
man/generate_qc_report.Rd
man/get_altexp_attributes.Rd
man/get_altexp_metadata.Rd
man/import_quant_data.Rd
man/integrate_fastmnn.Rd
man/integrate_harmony.Rd
man/integrate_sces.Rd
man/merge_altexp.Rd
man/merge_sce_list.Rd
man/metadata_to_coldata.Rd
man/miQC_nofilter.Rd
man/prepare_altexp_for_merge.Rd
man/prepare_merged_metadata.Rd
man/prepare_sce_for_merge.Rd
man/read_alevin.Rd
man/read_cellranger.Rd
man/read_kallisto.Rd
man/read_tximport.Rd
man/rowdata_to_df.Rd
man/sce_to_anndata.Rd
man/sce_to_seurat.Rd
man/scpcaTools-package.Rd
man/silhouette_width_from_pcs.Rd
man/sim_sce.Rd
man/within_batch_ari_from_pcs.Rd
renv.lock
renv/.gitignore
renv/activate.R
renv/settings.json
scpcaTools.Rproj
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/test-add_cell_mito_qc.R
tests/testthat/test-add_cellhash_calls.R
tests/testthat/test-add_gene_symbols.R
tests/testthat/test-add_miQC.R
tests/testthat/test-add_sample_metadata.R
tests/testthat/test-add_vireo_calls.R
tests/testthat/test-cluster_sce.R
tests/testthat/test-collapse_intron_counts.R
tests/testthat/test-filter_counts.R
tests/testthat/test-generate_qc_report.R
tests/testthat/test-integrate_sces.R
tests/testthat/test-integration_metrics.R
tests/testthat/test-merge_altexp.R
tests/testthat/test-merge_sce_list.R
tests/testthat/test-metadata_to_coldata.R
tests/testthat/test-read_alevin.R
tests/testthat/test-read_cellranger.R
tests/testthat/test-read_kallisto.R
tests/testthat/test-sce_to_anndata.R
tests/testthat/test-sce_to_seurat.R
tests/testthat/test-sim_sce.R
tests/testthat/test_report.Rmd
