fibertools-rs
Tools for fiberseq data written in rust.
File Explorer
Download Latest Version (.zip)- config.toml
- bug_report.md
- enhancement.md
- CI.yml
- release-plz.yml
- release-python-ma.yml
- release.yml
- center.png
- fiber_tools_grey.pdf
- fiber_tools_grey.png
- fiber_tools_teal.pdf
- fiber_tools_teal.png
- ft-extract-all.png
- logo.png
- burn_only_benchmark.md
- ft_0_12_pytorch.sh
- ft_0_12_pytorch_wrapper.sh
- ft_0_17_1_pytorch.sh
- ft_0_17_1_pytorch_factory_wrapper.sh
- ft_0_17_1_pytorch_sequential_wrapper.sh
- ft_0_17_1_pytorch_thread_local_wrapper.sh
- ft_0_17_1_pytorch_wrapper.sh
- README.md
- fetch-data.sh
- README.md
- RESULTS.md
- subcommands.rs
- 2.0_semi_torch.json
- 2.2_semi_torch.json
- 3.2_semi_torch.json
- convert-pt-to-onnx.py
- FIRE.conf.json
- FIRE.gbdt.json
- Revio_semi_torch.json
- mm-ml-per-group-passthrough.md
- fiberseq_to_ma.rs
- README.md
- __init__.py
- pysam_utils.py
- lib.rs
- test_molecular_annotation.py
- Cargo.toml
- DEV.md
- pyproject.toml
- README.md
- mod.rs
- parse.rs
- write.rs
- annotation.rs
- annotation_type.rs
- error.rs
- mod.rs
- primitives.rs
- view.rs
- build.rs
- coords.rs
- decode.rs
- iter.rs
- lib.rs
- liftover.rs
- serialize.rs
- tests.rs
- align.sh
- ref.fa.gz
- ref.fa.gz.fai
- ref.fa.gz.gzi
- test.cram
- test.cram.crai
- .gitignore
- Cargo.toml
- CHANGELOG.md
- LICENSE
- README.md
- CI.yml
- rtd_dark.css
- fiber_tools_grey.png
- layout.html
- basic-usage-examples.ipynb
- centered-plot.ipynb
- index.rst
- api.rst
- conf.py
- environment.yml
- index.rst
- make.bat
- Makefile
- requirements.txt
- __init__.py
- fiberplot.py
- plot.py
- utils.py
- fiberdata.rs
- lib.rs
- .gitignore
- Cargo.toml
- DEV-NOTES.md
- pyproject.toml
- README.md
- benchmark_opts.rs
- call_peaks_opts.rs
- center_opts.rs
- clear_kinetics_opts.rs
- convert_tags_opts.rs
- ddda_to_m6a_opts.rs
- decorator_opts.rs
- extract_opts.rs
- fire_opts.rs
- footprint_opts.rs
- mock_fire_opts.rs
- nucleosome_opts.rs
- pg_inject_opts.rs
- pg_lift_opts.rs
- pg_pansn_opts.rs
- pileup_opts.rs
- predict_opts.rs
- qc_opts.rs
- strip_basemods_opts.rs
- union_peaks_opts.rs
- validate_opts.rs
- mod.rs
- revio.onnx
- three_two.onnx
- two_two.onnx
- two_zero.onnx
- fdr.rs
- mod.rs
- peaks.rs
- add_nucleosomes.rs
- benchmark.rs
- center.rs
- clear_kinetics.rs
- convert_tags.rs
- ddda_to_m6a.rs
- decorator.rs
- extract.rs
- fire.rs
- footprint.rs
- mock_fire.rs
- pg_inject.rs
- pg_lift.rs
- pg_pansn.rs
- pileup.rs
- predict_m6a.rs
- qc.rs
- strip_basemods.rs
- union_peaks.rs
- validate.rs
- sorted_write.rs
- acf.rs
- bamannotations.rs
- basemods.rs
- bio_io.rs
- fibertig.rs
- fire.rs
- ftexpression.rs
- input_bam.rs
- ma_io.rs
- nucleosome.rs
- panspec.rs
- platform.rs
- cli.rs
- fiber.rs
- lib.rs
- main.rs
- subcommands.rs
- utils.rs
- all.bam
- all.bam.bai
- center.bam
- center.bam.bai
- center.bed
- center.small.bed
- ctcf-footprints.bed.gz
- ctcf.bam
- ctcf.bam.bai
- ctcf.bed.gz
- ctcf.yaml
- hg38.analysisSet.fa.fai
- ma_spelled.bam
- msp_nuc.bam
- NAPA.bam
- NAPA.bam.bai
- NAPA.rgn
- nuc_example.bam
- ONT.NAPA.bam
- ONT.NAPA.bam.bai
- revio.bam
- test.txt
- test.txt.gz
- three_two.bam
- two_two.bam
- regression__call_peaks__call_peaks_ctcf_snapshot.snap
- regression__center__center_default.snap
- regression__decorator__track_decorators_emit_fire_and_linker.snap
- regression__extract__extract_all_napa.snap
- regression__extract__extract_m6a.snap
- regression__extract__extract_msp.snap
- regression__extract__extract_nuc.snap
- regression__extract__extract_reads_ma_spelled_fixture.snap
- regression__fire__fire_extract_reports_fire_fdrs.snap
- regression__fire__fire_feats_to_text.snap
- regression__footprint__footprint_ctcf.snap
- regression__pileup__pileup_default.snap
- regression__pileup__pileup_m6a.snap
- regression__pileup__pileup_no_msp.snap
- regression__pileup__pileup_no_nuc.snap
- regression__predict_m6a__mm_strand_groups.snap
- regression__qc__qc_default.snap
- regression__qc__qc_m6a_per_msp_sees_fire_elements.snap
- call_peaks.rs
- center.rs
- common.rs
- convert_tags.rs
- decorator.rs
- extract.rs
- fire.rs
- footprint.rs
- mock_fire.rs
- pileup.rs
- predict_m6a.rs
- qc.rs
- union_peaks.rs
- bio_io.rs
- boundary_bug_test.rs
- call_peaks_test.rs
- coordinate_lift_test.rs
- extract_test.rs
- fiber_stream.rs
- fibertig_test.rs
- input_bam.rs
- m6a_prediction_test.rs
- molecular_annotation.rs
- nucleosome.rs
- regression.rs
- run_test.rs
- test-decorator.sh
- exclude.bed.gz
- positives.bed.gz
- ref.fa
- ref.fa.fai
- sample.bam
- sample.bam.bai
- config.yaml
- config.yaml
- hg38.gap.bed.gz
- SDs.merged.hg38.bed.gz
- ATAC.bed.gz
- download.sh
- GM12878-fire-v0.1-peaks-20-percent.bed.gz
- GM12878-fire-v0.1-peaks.bed.gz
- GM12878_DHS.bed.gz
- hotspots_ENCFF452DZE.bed.gz
- hotspots_ENCFF828AUX.bed.gz
- peaks_CTCF_ENCFF951PEM.bed.gz
- peaks_ENCFF073ORT.bed.gz
- peaks_ENCFF598KWZ.bed.gz
- env.yml
- config.yaml
- apply.smk
- common.smk
- features.smk
- regions.smk
- resources.smk
- trackhub.smk
- train.smk
- compare_models.py
- make_trackhub.py
- train-fire-model.py
- bed12_filter.as
- decoration.as
- Snakefile
- README.md
- .gitattributes
- .gitignore
- .pre-commit-config.yaml
- .readthedocs.yaml
- build.rs
- Cargo.lock
- Cargo.toml
- CHANGELOG.md
- CONTRIBUTING.md
- dist-workspace.toml
- README.md
- release-plz.toml
// repository documentation
Was this content helpful?
(0 ratings)