← Life Sciences NGS AnalysisSOURCE FILE ARCHIVE
Inside the package
Life Sciences NGS Analysis · 81 files · 283 KB · Sep 30, 2026 · 22:50 UTC
| File | Size |
|---|---|
.codex-plugin/plugin.jsonSHA-256d8a4bc590c865a6e374b41294c8fc942b6bc78dddf3ceedec37a639c99214406 | 2.45 KB |
README.mdSHA-256da752aa4f015accd11cb5d0faec03819486853849f10ce64122d4cee081b9b8e | 35.6 KB |
assets/app-icon.pngSHA-256de2f5931b97d9b2ce6325208dd514c69ee9bf13201af635d8fb17345a5ef4737 | 38.2 KB |
references/database-registry.jsonSHA-256f45698bd3506210b2388d43436d59d3c664254c72da23e3d7a4cb3f8e1f015f9 | 4.3 KB |
references/intake-schema.jsonSHA-25618df838e61075772f47480e66078143cb24c0b8d470beaeaa48583e5dad6626e | 3.89 KB |
references/pipeline-registry.jsonSHA-256637cacb20832184f47450a2d3246719ab633302f8334bc6e8eb49659675cc549 | 34.3 KB |
references/reference-registry.jsonSHA-256012308bf2230476929bdcaee74a19b071dd3d7a94805d1a6c37c4866d9c3f4cc | 3.09 KB |
references/run-envelope-schema.jsonSHA-2569cb5ea2a7cb98c740c5a33bee0443455dc71f89c23af4b69aa2a5c1b177ab76b | 2.19 KB |
references/runtime-install-guidance.mdSHA-2564ffd8ad79e3d25a5e2fcc3b642a109ecb7d6371f40f8e85f8fd388fb32862171 | 3.57 KB |
scripts/ngs_epigenomics_utils.pySHA-256eba7e72729f65375b0990a06fe0e15e3b44e62491813229a876726ff821208bf | 24.5 KB |
scripts/ngs_planner_utils.pySHA-256de1f03601f02b5f0b1d85d2bb77cb5b5853f901eca830a8b320985ac8a2d559f | 2.26 KB |
scripts/ngs_preflight.pySHA-256c5ccb0ce8758434dbb0f13a02d8bfe82e38a0b50b2f8b48be940f8cca6a3a197 | 14.9 KB |
scripts/ngs_reference_manager.pySHA-2564f86eb102b6f39d8429ff4a8162c6a5e84206a744eca4442662b44ddfb926e55 | 61.5 KB |
scripts/ngs_resource_gate.pySHA-2564b7e3e2f86a706268bc1516c625faab6af2191a8df3ec71a4fe92b6ea660c7a5 | 5.96 KB |
scripts/ngs_run_utils.pySHA-256ee2d718ee8faae162c9956af666ef148743894a10114cbcdc9170b182bb8b49c | 18.8 KB |
scripts/ngs_visualization_utils.pySHA-2560963e6b13bc93077454d4905d08efc01dd1a8bfb518aea6e091e32fc4db5315d | 24.9 KB |
scripts/run_amplicon_microbiome.pySHA-2564855299906262de5bd207a9199c942d44fafc4a6b968fa11202b2ab88058eeb7 | 46 KB |
scripts/run_atacseq_peaks_qc.pySHA-256d3f5934b56b961a2e3028bc7f03f6c5f5657cf95edf4bc56ad1d48f38194886c | 28.1 KB |
scripts/run_bcl_to_fastq.pySHA-256fbfcdfd27b5c70d8908d4b678af63a93567118b8f175f8273c74ce1298fbda1d | 30.1 KB |
scripts/run_bulk_rnaseq_counts_qc.pySHA-25620c37829b99ebf1c5ecc35c96036f5429fb5bd3709f084bf22456000d5f2c8ed | 40.3 KB |
scripts/run_bulk_rnaseq_de.pySHA-256749e5a4f92edde3bce4af5c9d843a8e687d240d758f7f90a2f97481284d9322e | 26.9 KB |
scripts/run_chip_cutrun_peaks_qc.pySHA-256027bf7ed28de85789f9f9903ac61b6efd0a75fcfe8e68c3a922346efcf148a59 | 30 KB |
scripts/run_dna_germline_variants.pySHA-256f32fe49fbb81e2e1af29184db9fa41378f2fa3b2231627e5147e6cac697a4da9 | 24.7 KB |
scripts/run_dna_somatic_variants.pySHA-2567962d6c004da4a35909e772659c2a955d6353ad325b98f820b4ac0b5298c15ef | 32 KB |
scripts/run_dna_umi_panel_variants.pySHA-256c8674a9715c3ccf83cd246298814a1f75a51f79c947887a63c469ea0555b2557 | 39.5 KB |
scripts/run_dna_variant_calling.pySHA-256b6d341c9013f9e05bf0184bec69f8a3210e90cb2c8b704f81a07825fedc54a26 | 41.4 KB |
scripts/run_fastq_assay_package.pySHA-2560b4dfc980a2c43ee40cb1813ec07f84b53798aa1afb1427ee2489832bf416043 | 128 KB |
scripts/run_fastq_qc.pySHA-256de8db8501b6724bbbca67463d4214fc4138cc74b281ce61c0b9ca32d7799cc5f | 45.7 KB |
scripts/run_nfcore_pipeline.pySHA-25634c9fae1bb207be55f2db2de9ad9deab50634bf19a635077953d1b21cff5f009 | 20.3 KB |
scripts/run_scrnaseq_fastq_to_count.pySHA-2560482df605ccc084ed457261461ff515d9de3f5903d7555517697538202de92aa | 33 KB |
scripts/run_scrnaseq_post_count_qc.pySHA-256756a4f72cd01c75f4d5379017ee3866105468ba7cc203b9d9470dee885073568 | 50.7 KB |
scripts/run_shotgun_metagenomics.pySHA-256e5457cbc08578e4153ef47f79e0e52be7698899a659420f48b08e8fae733b911 | 55.5 KB |
skills/ngs-amplicon-microbiome/SKILL.mdSHA-2564e60f815623855ba2fd78ce0cfbb289f5cecb169693c411d6a03702df579d5cc | 5.66 KB |
skills/ngs-amplicon-microbiome/agents/openai.yamlSHA-256828d98418d5c195dd7880a22a598e173d6950adbd3083d62d793827fb89cc36f | 267 Bytes |
skills/ngs-analysis-router/SKILL.mdSHA-2560a6ce8bdb7e45d69c4439032c775a3185f38879d0b1a03c3b36382e98e543a95 | 4.31 KB |
skills/ngs-analysis-router/agents/openai.yamlSHA-256fc88c8730f7703990fda1123fe7f9f7e5b7551b3baa647ba8027ae53c443529b | 296 Bytes |
skills/ngs-atacseq-peaks-qc/SKILL.mdSHA-256d9ff2e1e3798d8b4ae286e0de550acbec9875a3573c51a6bd231292d71df0a6e | 3.45 KB |
skills/ngs-atacseq-peaks-qc/agents/openai.yamlSHA-256040871dcf48efe0f95e18571a8ec27b166f6b5ba05c70bb8a2085a0f36f50fbd | 270 Bytes |
skills/ngs-bcl-to-fastq/SKILL.mdSHA-25602c0cc840bc3bb2dc0c01ae1f62cfb21203ea7f72a70fb9f3bbfb6ea0bab9f86 | 3.85 KB |
skills/ngs-bcl-to-fastq/agents/openai.yamlSHA-2565b15cd38804aef5b9dbe13d4dea65d0c92a94bf65dbb55c051fe9c7770bda456 | 291 Bytes |
skills/ngs-bulk-rnaseq-counts-qc/SKILL.mdSHA-25681b18ef7f03bd3ae6e1742a35cadb443a48122e37613e57c40af2ee6352bb322 | 3.94 KB |
skills/ngs-bulk-rnaseq-counts-qc/agents/openai.yamlSHA-25629c9967bf14db026f3524bc529c688e311575dcb4fee1f8305d52af94b543973 | 291 Bytes |
skills/ngs-bulk-rnaseq-differential-expression/SKILL.mdSHA-2560726a62fb607beef7a19efaf9972821a1fe7127f9f0cca5934d1d16b4aa37a07 | 3.46 KB |
skills/ngs-bulk-rnaseq-differential-expression/agents/openai.yamlSHA-256ed08ae692bc1002aba4fc63b247f6644b8354f809d1c9dcf1cbe704f7ee346da | 268 Bytes |
skills/ngs-bulk-rnaseq/SKILL.mdSHA-25630a55e6d8f88bcb2025b997d414c9a875383d3a7c232cb9eccdbc10de107788e | 3.62 KB |
skills/ngs-bulk-rnaseq/agents/openai.yamlSHA-2562083a12bf7e933575c5f0bcc37c5733753711df910e5de1d47cf54e9754fa09c | 296 Bytes |
skills/ngs-chip-cutrun-peaks-qc/SKILL.mdSHA-2564718713903b0d22deab18ab4de0725e98efaa61e7bb504bd0ee0965cb00a601c | 3.67 KB |
skills/ngs-chip-cutrun-peaks-qc/agents/openai.yamlSHA-25621a220f85f1f0dfaf4a8c2f7af594b3c3610eb880667229bf77400cf524dad5a | 292 Bytes |
skills/ngs-dna-germline-variants/SKILL.mdSHA-256c1370a2b238be8434e9835f9417e9fd556657126d0c84754ed134610097b8fda | 3.72 KB |
skills/ngs-dna-germline-variants/agents/openai.yamlSHA-25681a4646020fe51e6bab383f5d341a6f2e4a2c9654684b910aaa47675498327db | 300 Bytes |
skills/ngs-dna-somatic-variants/SKILL.mdSHA-256b7c01ec7aca4cc40485977ca310015a3e9169c9348fcb9fc3009176ae8e58f5a | 3.72 KB |
skills/ngs-dna-somatic-variants/agents/openai.yamlSHA-2565ff936aab8b89f2ed85ea883cd18b9631000d55c39d348d8c35f4a0a40e3db58 | 302 Bytes |
skills/ngs-dna-umi-panel-variants/SKILL.mdSHA-256ac2bdf3635ec159cd386e2597383a5d89fced4eaf772727b1fa0b5497de6d374 | 3.71 KB |
skills/ngs-dna-umi-panel-variants/agents/openai.yamlSHA-256d26a0e5e833608653da7460854587288df51452a3f8cfb547994e78217f22afe | 291 Bytes |
skills/ngs-dna-variant-calling/SKILL.mdSHA-2562e0e6be347bd672114e18c15dcd1d50ac6e94f76932325d9e706261283c3a1b2 | 3.67 KB |
skills/ngs-dna-variant-calling/agents/openai.yamlSHA-2562660ed126627e867fbe321862dc49e6511e529ae859fb3a269a55ac5301794f9 | 285 Bytes |
skills/ngs-epigenomics-peaks/SKILL.mdSHA-256a4ef255e0e6b861b55b6250bb748131a6e2c18457b03348fd93bddf29736ff3c | 2.5 KB |
skills/ngs-epigenomics-peaks/agents/openai.yamlSHA-2562e2aacf548ea922b8667fde3783c24e74b902a758c9c701981219263e2ad7ae9 | 277 Bytes |
skills/ngs-fastq-qc/SKILL.mdSHA-2564cb6a3f454e07d6ea5cc483537c4656abbcef2e3eb6316fc727f9d506fe0b864 | 4.28 KB |
skills/ngs-fastq-qc/agents/openai.yamlSHA-256936297fe015cc945ce3be8ba4ab4fcb1407ab4044916bbd0ee93a25f4afb27e7 | 253 Bytes |
skills/ngs-runtime-env/SKILL.mdSHA-2568bf0d5d2d06c4dd4b78ecc15786ded516fdf4b0157a0fbb50221ff47c188be95 | 6.23 KB |
skills/ngs-runtime-env/agents/openai.yamlSHA-256c0a9c9dea08a1cf292f44e38aa23c912a60848641b5ca76f83d3fd78d3bf1276 | 262 Bytes |
skills/ngs-scrna-seq/SKILL.mdSHA-25630b8d1d9524a8cd90e7609a8e511299bac4f7543d9d038cfb68c062a6b4ff0ba | 3.78 KB |
skills/ngs-scrna-seq/agents/openai.yamlSHA-2566be5b4d9b57e819ba6a8da69899ea229657599f498edfd1d0375cd7f50b6a420 | 285 Bytes |
skills/ngs-shotgun-metagenomics/SKILL.mdSHA-256e17b2e52275d360980a7f7a37a1c452796f359bb546edca1b53744e07d4943dc | 4.77 KB |
skills/ngs-shotgun-metagenomics/agents/openai.yamlSHA-2567f47e4ba2c6b90ba0ca54fbc381d3173de0c27392fff8e9edd45045070d0ccea | 288 Bytes |
skills/scrna-seq-qc/SKILL.mdSHA-25693f9280a6a8956368926152489397b4dde81b7672ee8a49a8b1060fd9f634939 | 8.14 KB |
skills/scrna-seq-qc/agents/openai.yamlSHA-256e3d2f2b13ab4e4f0b3a240927b33cd84b7fc3062037b943453417059c510f7ee | 267 Bytes |
skills/scrna-seq-qc/references/qc-annotation-umap-heuristics.mdSHA-2568c74d2478add12c83b4bc51e27504f3b0239844a472d4060fc256f2553a50497 | 8.59 KB |
tests/test_bcl_to_fastq_runner.pySHA-25635120f1f18816dc3fcfb9b9d84c6eff07c8d8b25c7642bcc10329391d35d913a | 6.59 KB |
tests/test_bulk_rnaseq_counts_qc_runner.pySHA-2566b04ddbbda7ff91810e8afacd13b348f6d1803f4a07b012e7e75a8d91abfd65f | 6.62 KB |
tests/test_new_backend_planners.pySHA-25670e8ded6adf55c88179e0b176c88bb1a03a1a3b4dd062491b57dd66bc4efa8e6 | 47.4 KB |
tests/test_ngs_preflight.pySHA-2568bfa3986cb703e19d2e9fda42219c9c8b87e815b9ef777329d3362e97eec98e3 | 2.73 KB |
tests/test_scrnaseq_post_count_qc_runner.pySHA-2565d13bae970be9873577d9f47b053e5b4995145e2aa233cab9782396f9f5cb2e9 | 2.65 KB |
workflows/amplicon_microbiome/run_dada2_backend.RSHA-25697bbad088836f5931c1ecb99182df42536d7a544ab9b14429989bf95d4218e1f | 7.67 KB |
workflows/bulk_rnaseq_counts_qc/Snakefile.smkSHA-256ca8c59612f4740dc54d1b22b8c7acef76a84e5913bbf54dfd395c5af94e80df8 | 3.63 KB |
workflows/bulk_rnaseq_counts_qc/aggregate_salmon_quant.pySHA-256208d907e1156e7e483d973c7d3ac234fd85a4292910dda3df277b6f31f5625cf | 6.26 KB |
workflows/bulk_rnaseq_differential_expression/run_bulk_de.RSHA-256775741b0edb03e3e92d82d4e8c8eda713a961791d30aaac9baa33cff8a055c99 | 20 KB |
workflows/scrnaseq_fastq_to_count/Snakefile.smkSHA-256de94cef29187b794e5e17b2855abdebfe1823883f0bacf9e4ca7e0c43a4cf2c9 | 2.05 KB |
workflows/scrnaseq_fastq_to_count/run_star_genome_generate.pySHA-256153860c1661e96127c1834d8ef8e04bc02ab980d3e8646a74475409117ded391 | 1.74 KB |
workflows/scrnaseq_fastq_to_count/run_starsolo.pySHA-256042a1ed11291484efd0eac039bcbccb8e3e825fc626facb0026fd5c0d4deeb18 | 3.91 KB |
Files are archived as data; their code has not been executed. The package does not include private remote service code.