.gitignore
AGENTS.md
LICENSE
README.md
build.sh
meta.yaml
pyproject.toml
run_test.sh
setup.py
Data/Gene.gtf
Data/TE.bed
Data/test.bam
bin/scTE
bin/scTEATAC
bin/scTEATAC_build
bin/scTE_build
docs/scTE.png
example/Figure3/1.pack.py
example/Figure3/2.norm_and_learn.py
example/Figure3/3.diffexp.py
example/Figure3/4.plots-allgenes.py
example/Figure3/4.plots-alltes.py
example/Figure3/4.plots-specific-tes.py
example/Figure3/5.marker_genes-leiden-0.2.py
example/Figure3/5.marker_genes-small-grp_cut.py
example/Figure3/5.marker_genes-small.py
example/Figure3/5.marker_genes.py
example/Figure3/TE_genes_id.mm10.txt.gz
example/Figure3/0.cluster_scripts/scte/do_batch.sh
example/Figure3/0.cluster_scripts/scte/scte.sh
example/Figure3/0.cluster_scripts/starsolo/do_batch.sh
example/Figure3/0.cluster_scripts/starsolo/starsolo.sh
scTE/__init__.py
scTE/_version.py
scTE/annotation.py
scTE/base.py
scTE/scatacseq.py
scTE/miniglbase/README.md
scTE/miniglbase/__init__.py
scTE/miniglbase/base_genelist.py
scTE/miniglbase/config.py
scTE/miniglbase/genelist.py
scTE/miniglbase/location.py
scTE/miniglbase/utils.py
scte_quant.egg-info/PKG-INFO
scte_quant.egg-info/SOURCES.txt
scte_quant.egg-info/dependency_links.txt
scte_quant.egg-info/not-zip-safe
scte_quant.egg-info/requires.txt
scte_quant.egg-info/top_level.txt