blobtoolkit/blobtoolkit-4.1.5.zip
blobtoolkit-blobtoolkit-a63e5a5
.bumpversion.cfg
869 Bytes
.coveragerc
200 Bytes
.github
dependabot.yml
329 Bytes
workflows
build-api.yml
1.2 kB
build-blobtoolkit-dependencies.yml
1.6 kB
build-blobtoolkit.yml
1.3 kB
build-ui.yml
1.2 kB
changes.yml
8.1 kB
conditional-workflow.yml
5.4 kB
github-release.yml
722 Bytes
package-api.yml
373 Bytes
package-blobtools.yml
2.2 kB
package-host.yml
3.1 kB
package-pipeline.yml
2.4 kB
package-ui.yml
370 Bytes
update-dependencies.yml
875 Bytes
upload-to-pypi.yml
834 Bytes
.gitignore
153 Bytes
.hostbumpversion.cfg
186 Bytes
.pipelinebumpversion.cfg
320 Bytes
.pre-commit-config.yaml
310 Bytes
.prebumpversion.cfg
65 Bytes
.pylintrc
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.pylintrc_tests
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.travis.yml
746 Bytes
AUTHORS
258 Bytes
LICENSE
1.1 kB
MANIFEST.in
334 Bytes
README.md
4.8 kB
bump_full_version.sh
672 Bytes
bump_npm_version.sh
730 Bytes
bump_versions.sh
3.0 kB
conftest.py
339 Bytes
databases
README.md
597 Bytes
uniprot
README.md
1.4 kB
all.dmnd
25.2 MB
gfLaeSulp1.1.buscogenes.dmnd
14.4 MB
gfLaeSulp1.1.buscoregions.dmnd
14.6 MB
ilEraDefo1.1.buscogenes.dmnd
18.8 MB
ilEraDefo1.1.buscoregions.dmnd
16.7 MB
mCerEla1.1.buscogenes.dmnd
14.4 MB
mCerEla1.1.buscoregions.dmnd
15.9 MB
mMelMel3.1.buscogenes.dmnd
14.4 MB
mMelMel3.1.buscoregions.dmnd
15.9 MB
examples
assembly.fasta
292.0 kB
assembly.reads.bam
2.6 kB
blast.out
6.8 kB
blobDB.json
8.2 kB
busco.tsv
20.6 kB
diamond.out
595 Bytes
list.json
198 Bytes
meta.yaml
226 Bytes
reads_1.fq.gz
1.1 kB
reads_2.fq.gz
1.1 kB
package-api.sh
116 Bytes
package-ui.sh
215 Bytes
pip_install_latest.sh
575 Bytes
pre-commit.sh
252 Bytes
pyproject.toml
294 Bytes
requirements.txt
147 Bytes
run_tests.sh
1.1 kB
setup.cfg
954 Bytes
setup.py
9.1 kB
src
api
.env.dist
197 Bytes
api.md
5.8 kB
package-lock.json
410.4 kB
package.json
1.4 kB
package.sh
449 Bytes
src
api-spec.yaml
18.8 kB
app.js
733 Bytes
app.test.js
170 Bytes
config
main.js
2.6 kB
swagger.js
588 Bytes
functions
io.js
2.7 kB
io.spec.js
1.4 kB
logger.js
1.6 kB
models
dataset.js
10.8 kB
dataset.spec.js
3.8 kB
field.js
1.8 kB
field.spec.js
8.7 kB
repository.js
304 Bytes
repository.spec.js
642 Bytes
public
index.html
377 Bytes
routes
dataset.js
1.9 kB
field.js
1.2 kB
identifier.js
539 Bytes
image.js
2.5 kB
search.js
11.8 kB
search_routes.js
15.7 kB
status.js
378 Bytes
summary.js
528 Bytes
table.js
4.4 kB
server.js
2.5 kB
shared
functions
utils.js
2.3 kB
utils.spec.js
4.6 kB
models
dataset.js
1.3 kB
field.js
3.3 kB
filter.js
2.3 kB
filter.spec.js
11.7 kB
repository.js
171 Bytes
repository.spec.js
404 Bytes
blobtoolkit-host
MANIFEST.in
142 Bytes
pip_install_latest.sh
602 Bytes
pyproject.toml
294 Bytes
requirements.txt
27 Bytes
setup.py
4.9 kB
src
__init__.py
42 Bytes
__main__.py
92 Bytes
blobtoolkit_host.py
46 Bytes
lib
__init__.py
72 Bytes
host.py
8.9 kB
version.py
91 Bytes
blobtoolkit-pipeline
MANIFEST.in
184 Bytes
pip_install_latest.sh
618 Bytes
pyproject.toml
294 Bytes
requirements.txt
153 Bytes
setup.py
5.8 kB
src
README.md
11.0 kB
__init__.py
19 Bytes
blobtoolkit-snakefiles
add_reads.smk
922 Bytes
blastn.smk
936 Bytes
blobtoolkit.smk
1.2 kB
blobtools.smk
1.5 kB
busco.smk
1.0 kB
chunk_stats.smk
973 Bytes
cov_stats.smk
1.0 kB
diamond.smk
930 Bytes
diamond_blastp.smk
847 Bytes
minimap.smk
953 Bytes
rules
_transfer_dataset.smk
597 Bytes
add_cov_to_tsv.smk
570 Bytes
add_summary_to_metadata.smk
431 Bytes
checksum_files.smk
545 Bytes
chunk_fasta.smk
891 Bytes
chunk_fasta_by_busco.smk
1.1 kB
chunk_nohit_fasta.smk
879 Bytes
combine_stats.smk
576 Bytes
count_busco_genes.smk
772 Bytes
extract_busco_genes.smk
773 Bytes
extract_nohit_fasta.smk
831 Bytes
generate_images.smk
887 Bytes
generate_summary.smk
467 Bytes
get_chunked_stats.smk
960 Bytes
get_window_stats.smk
626 Bytes
run_bamtools_stats.smk
500 Bytes
run_blastn.smk
2.1 kB
run_blobtk_depth.smk
601 Bytes
run_blobtools_add.smk
1.4 kB
run_blobtools_create.smk
2.0 kB
run_busco5.smk
2.3 kB
run_diamond_blastp.smk
1.3 kB
run_diamond_blastx.smk
1.3 kB
run_minimap2_align.smk
971 Bytes
run_minimap2_index.smk
745 Bytes
run_mosdepth.smk
665 Bytes
run_sub_pipeline.smk
2.3 kB
run_windowmasker.smk
970 Bytes
skip_windowmasker.smk
480 Bytes
unchunk_blastn.smk
569 Bytes
unchunk_blastx.smk
610 Bytes
unzip_assembly_fasta.smk
380 Bytes
validate_dataset.smk
757 Bytes
view.smk
1.7 kB
window_stats.smk
888 Bytes
windowmasker.smk
906 Bytes
blobtoolkit_pipeline.py
1.8 kB
lib
__init__.py
72 Bytes
add_summary_to_metadata.py
4.7 kB
chunk_fasta.py
11.6 kB
count_busco_genes.py
3.8 kB
data.py
787 Bytes
extract_busco_genes.py
3.7 kB
functions.py
7.2 kB
generate_config.py
25.2 kB
generate_configs.sh
327 Bytes
generate_static_images.py
5.2 kB
lsf_wrapper.sh
2.0 kB
resume_pipeline.py
4.8 kB
run.py
3.3 kB
run_btk_pipeline.sh
1.5 kB
track_bioproject_accessions.py
4.1 kB
transfer_completed.py
6.1 kB
unchunk_blast.py
2.6 kB
version.py
95 Bytes
window_stats.py
7.2 kB
blobtools
__init__.py
354 Bytes
__main__.py
92 Bytes
blobtools.py
3.7 kB
lib
__init__.py
208 Bytes
add.py
9.1 kB
bed.py
19.6 kB
blob_db.py
9.8 kB
busco.py
4.7 kB
calc.py
3.0 kB
cov.py
8.4 kB
dataset.py
8.8 kB
fasta.py
4.7 kB
fetch.py
3.1 kB
field.py
11.9 kB
file_io.py
3.9 kB
filter.py
19.0 kB
hits.py
25.2 kB
host.py
141 Bytes
key.py
1.1 kB
link.py
1.5 kB
remove.py
3.8 kB
synonyms.py
2.4 kB
taxdump.py
3.7 kB
taxid.py
1.2 kB
text.py
13.2 kB
trnascan.py
2.0 kB
validate.py
12.3 kB
version.py
86 Bytes
view.py
17.8 kB
btk
__init__.py
138 Bytes
__main__.py
86 Bytes
btk.py
2.3 kB
lib
pipeline.py
178 Bytes
version.py
86 Bytes
data
.bumpversion.cfg
1.7 kB
MANIFEST.in
137 Bytes
example
FXWY01
ERR1656467_cov.json
2.0 kB
ERR1656467_read_cov.json
1.6 kB
bestsumorder_class.json
1.2 kB
bestsumorder_class_cindex.json
987 Bytes
bestsumorder_class_positions.json
280.3 kB
bestsumorder_class_score.json
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bestsumorder_family.json
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bestsumorder_family_cindex.json
987 Bytes
bestsumorder_family_positions.json
286.6 kB
bestsumorder_family_score.json
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bestsumorder_genus.json
1.5 kB
bestsumorder_genus_cindex.json
987 Bytes
bestsumorder_genus_positions.json
287.6 kB
bestsumorder_genus_score.json
1.6 kB
bestsumorder_kingdom.json
1.0 kB
bestsumorder_kingdom_cindex.json
987 Bytes
bestsumorder_kingdom_positions.json
279.2 kB
bestsumorder_kingdom_score.json
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bestsumorder_order.json
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bestsumorder_order_cindex.json
987 Bytes
bestsumorder_order_positions.json
282.8 kB
bestsumorder_order_score.json
1.6 kB
bestsumorder_phylum.json
1.1 kB
bestsumorder_phylum_cindex.json
987 Bytes
bestsumorder_phylum_positions.json
279.5 kB
bestsumorder_phylum_score.json
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bestsumorder_positions.json
292.5 kB
bestsumorder_species.json
2.1 kB
bestsumorder_species_cindex.json
987 Bytes
bestsumorder_species_positions.json
295.0 kB
bestsumorder_species_score.json
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bestsumorder_superkingdom.json
1.0 kB
bestsumorder_superkingdom_cindex.json
987 Bytes
bestsumorder_superkingdom_positions.json
279.2 kB
bestsumorder_superkingdom_score.json
1.6 kB
eukaryota_odb9_busco.json
12.0 kB
gc.json
1.9 kB
identifiers.json
3.9 kB
length.json
1.7 kB
meta.json
15.6 kB
metazoa_odb9_busco.json
24.4 kB
ncount.json
1.1 kB
nematoda_odb9_busco.json
35.7 kB
pip_install_latest.sh
533 Bytes
pyproject.toml
294 Bytes
requirements.txt
14 Bytes
schema
basic.schema.json
1.3 kB
meta.schema.json
1.3 kB
subschemas
array.data.schema.json
509 Bytes
array.meta.schema.json
506 Bytes
assembly.basic.schema.json
1.1 kB
assembly.schema.json
1.1 kB
category.data.schema.json
536 Bytes
category.meta.schema.json
340 Bytes
fields.schema.json
2.6 kB
identifier.data.schema.json
446 Bytes
identifier.meta.schema.json
348 Bytes
multiarray.data.schema.json
585 Bytes
multiarray.meta.schema.json
521 Bytes
plot.schema.json
698 Bytes
reads.schema.json
1.2 kB
taxon.basic.schema.json
419 Bytes
taxon.schema.json
445 Bytes
variable.data.schema.json
363 Bytes
variable.meta.schema.json
866 Bytes
setup.py
2.9 kB
demo
FXWY01
ERR1656467_cov.json
2.0 kB
ERR1656467_read_cov.json
1.6 kB
bestsumorder_class.json
1.2 kB
bestsumorder_class_cindex.json
987 Bytes
bestsumorder_class_positions.json
280.3 kB
bestsumorder_class_score.json
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bestsumorder_family.json
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bestsumorder_family_cindex.json
987 Bytes
bestsumorder_family_positions.json
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bestsumorder_family_score.json
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bestsumorder_genus.json
1.5 kB
bestsumorder_genus_cindex.json
987 Bytes
bestsumorder_genus_positions.json
287.6 kB
bestsumorder_genus_score.json
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bestsumorder_kingdom.json
1.0 kB
bestsumorder_kingdom_cindex.json
987 Bytes
bestsumorder_kingdom_positions.json
279.2 kB
bestsumorder_kingdom_score.json
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bestsumorder_order.json
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bestsumorder_order_cindex.json
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bestsumorder_order_positions.json
282.8 kB
bestsumorder_order_score.json
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bestsumorder_phylum.json
1.1 kB
bestsumorder_phylum_cindex.json
987 Bytes
bestsumorder_phylum_positions.json
279.5 kB
bestsumorder_phylum_score.json
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bestsumorder_positions.json
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bestsumorder_species.json
2.1 kB
bestsumorder_species_cindex.json
987 Bytes
bestsumorder_species_positions.json
295.0 kB
bestsumorder_species_score.json
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bestsumorder_superkingdom.json
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bestsumorder_superkingdom_cindex.json
987 Bytes
bestsumorder_superkingdom_positions.json
279.2 kB
bestsumorder_superkingdom_score.json
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eukaryota_odb9_busco.json
12.0 kB
gc.json
1.9 kB
identifiers.json
3.9 kB
length.json
1.7 kB
meta.json
15.6 kB
metazoa_odb9_busco.json
24.4 kB
ncount.json
1.1 kB
nematoda_odb9_busco.json
35.7 kB
generate_btk_plots.sh
4.2 kB
docker
Dockerfile
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_-linux
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_.whl
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api
.env
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Dockerfile
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blobtools
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env.yaml
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dependencies
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env.yaml
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setup.sh
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startup.sh
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env.yaml
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setup.sh
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startup.sh
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viewer
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Dockerfile
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packaged-viewer
package-lock.json
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package.json
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package.sh
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src
app.js
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viewer
.babelrc
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.bumpversion.cfg
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.env.dist
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.prettierignore
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AUTHORS
264 Bytes
CHANGELOG.md
489 Bytes
INSTALL.md
67 Bytes
LICENSE
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README.md
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package-lock.json
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package.json
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package.sh
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postcss.config.js
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src
client
favicon
android-chrome-192x192.png
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android-chrome-512x512.png
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apple-touch-icon.png
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favicon-16x16.png
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favicon-32x32.png
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favicon.ico
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manifest.json
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index.html
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main.js
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views
actions
dataset.js
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components
App.jsx
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App.scss
645 Bytes
AxisTitle.jsx
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BTKLogos.jsx
726 Bytes
Busco.jsx
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BuscoData.jsx
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BuscoPlot.jsx
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CanvasCircle.jsx
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Caption.scss
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CategoryDistribution.jsx
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CategoryLegend.jsx
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CategoryPlotBoundary.jsx
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CircleAxis.jsx
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CumulativePlot.jsx
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CumulativePlotBoundary.jsx
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Customise.scss
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CustomiseDatasetTable.jsx
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DOIBadge.jsx
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Dataset.jsx
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DatasetApplyFilters.jsx
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DatasetCreateList.jsx
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DatasetModal.jsx
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DatasetSpinner.jsx
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DatasetTable.jsx
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DatasetTableCSV.jsx
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DatasetTree.jsx
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Datasets.scss
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DetailPlot.jsx
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Error.jsx
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ExportButton.jsx
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ExternalLink.jsx
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FAQ.scss
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FAQs.jsx
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Field.jsx
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FieldBox.jsx
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FieldBoxHeader.jsx
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FieldBoxHeaderButton.jsx
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FieldBoxHeaderFilterButtons.jsx
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FieldRawDataPreview.jsx
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FieldSet.jsx
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Fields.scss
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FigureCaption.jsx
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Filter.jsx
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FilterBox.jsx
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FilterBoxHeader.jsx
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FilterCategory.jsx
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FilterControlCategory.jsx
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FilterControlRange.jsx
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FilterDisplayCategory.jsx
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FilterDisplayRange.jsx
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FilterPreview.jsx
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Filters.jsx
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Filters.scss
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FindDatasets.jsx
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GetStarted.jsx
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Header.jsx
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HomePage.jsx
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HomePage.scss
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Icon.scss
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LassoSelect.jsx
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Layout.jsx
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Layout.scss
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LayoutControls.jsx
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LayoutHeader.jsx
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LayoutPlots.jsx
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Link.jsx
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ListModal.jsx
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Main.jsx
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MainPlot.jsx
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MainPlotBoundary.jsx
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MenuDatasetMain.jsx
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Palette.scss
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PaletteSwatch.jsx
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PlotAxisTitle.jsx
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PlotBubbles.jsx
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PlotBubblesCanvas.jsx
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Tree.scss
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XPlot.jsx
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YPlot.jsx
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img
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ebi-logo.png
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figure1.jpg
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figure2.jpg
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hex_blur.jpg
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sanger-logo.png
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uoe-logo.png
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style
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svg
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category.svg
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circleStyle.svg
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clone.svg
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fontSize.svg
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gridShape.svg
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invert.svg
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kiteShape.svg
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kiteSolid.svg
2.3 kB
lineShape.svg
2.9 kB
lineStyle.svg
2.4 kB
linear.svg
2.1 kB
log.svg
2.4 kB
max.svg
2.4 kB
mean.svg
2.7 kB
min.svg
2.4 kB
mixedStyle.svg
2.8 kB
scale.svg
2.7 kB
selectAll.svg
3.4 kB
selectNone.svg
3.3 kB
show.svg
5.3 kB
showHide.svg
5.5 kB
sqrt.svg
2.6 kB
squareShape.svg
2.9 kB
sum.svg
2.6 kB
sumActive.svg
2.6 kB
svg.svg
2.4 kB
test.svg
1.6 kB
weather.svg
71.7 kB
xAxis.svg
1.9 kB
xLetter.svg
2.4 kB
yAxis.svg
1.9 kB
yLetter.svg
2.4 kB
zAxis.svg
2.1 kB
zero.svg
2.4 kB
containers
Palettes.jsx
1.1 kB
index.jsx
454 Bytes
layouts
default.jsx
274 Bytes
querySync.jsx
17.9 kB
reducers
api.js
872 Bytes
color.js
3.8 kB
dataset.js
1.8 kB
datasetTable.js
11.5 kB
datasetTree.js
8.6 kB
dimension.js
1.4 kB
field.js
21.9 kB
filter.js
12.1 kB
gdpr.js
253 Bytes
hexFunctions.js
1.8 kB
history.js
283 Bytes
identifiers.js
2.0 kB
list.js
6.4 kB
location.js
7.4 kB
plot.js
1.5 kB
plotData.js
50.3 kB
plotHexBins.js
6.9 kB
plotOverlay.js
1.4 kB
plotParameters.js
16.7 kB
plotSquareBins.js
12.1 kB
plotStyles.js
3.6 kB
preview.js
8.6 kB
record.js
7.7 kB
reference.js
5.4 kB
repository.js
12.3 kB
root.js
2.4 kB
select.js
3.8 kB
selectTools.js
1.4 kB
selectorCreators.js
617 Bytes
summary.js
50.2 kB
tracking.js
1.6 kB
store.jsx
476 Bytes
config
client.js
256 Bytes
environment.js
31 Bytes
main.js
2.4 kB
swagger.js
588 Bytes
public
index.html
377 Bytes
webpack.config.js
5.6 kB
tests
files
TEST
gc.json
9.9 kB
identifiers.json
20.0 kB
length.json
9.3 kB
meta.json
889 Bytes
ncount.json
5.3 kB
UELW01.busco.actinopterygii_odb10.tsv
455.3 kB
infile
17 Bytes
infile.gz
44 Bytes
unit_tests
test_field.py
7.7 kB
test_file_io.py
2.6 kB
test_taxdump.py
989 Bytes
test_taxid.py
1.7 kB
tox.ini
2.1 kB