3d83069adaff81331c4c2e849ca3aeb6 *DESCRIPTION
55546d7198e0b4536025bb58282a6d9f *NAMESPACE
e73d99742effb8bae8a45ed394f7977c *R/AbForests_AntibodyForest.R
ed72fd295542859bb8bfa77ea0023e7f *R/AbForests_CompareForests.R
f3c8bba8fcc3906ff8c23f9cc4f24536 *R/AbForests_ConvertStructure.R
5b14be381c3522d34d7c8a2667adbc1e *R/AbForests_CsvToDf.R
dbe352b77605475c60644231e60ec692 *R/AbForests_ForestMetrics.R
7a6f42a7dc2e47c8d7bf34aef2e313c6 *R/AbForests_PlotGraphs.R
fa7d30971a78653b2c8c48180f46b1ef *R/AbForests_PlyloToMatrix.R
3bb881b6fea868fa0957360d54c8fe1c *R/AbForests_RemoveNets.R
1efa4b2375ae3056e589f80c86f1798c *R/AbForests_SubRepertoiresByCells.R
14640d367455fdfdacd9e4db0ca812c2 *R/AbForests_SubRepertoiresByUniqueSeq.R
93d30c9b398be54bb234d7d4fcbccc89 *R/AbForests_UniqueAntibodyVariants.R
d7060c6a63422cc55a722260771b6018 *R/AbForests_data.R
50922049b263e6bff74260ea85801e2c *R/AbForests_internal.R
3e298a41e61abb1f081703e31a3bf2f1 *R/Echidna_Internal_functions.R
d77e781f8570e9753d0f76503019f709 *R/Echidna_data.R
5a325b94054f39710db6e3817b542793 *R/Echidna_other_functions.R
83331c727af78c8b075ae549b612d36a *R/Echidna_simulate_repertoire.R
6b0e52d41aa1c00a37b2bc0aa7df2e44 *R/Echidna_vae_generate.R
d426bde298042f9ec1c4a0028f61cb56 *R/Echidna_vae_internal_functions.R
8ec92f235cc43ae22a6206e41af061e4 *R/GEX_DEgenes.R
d7f0acc28d8a0a9b9830c6049f3c683b *R/GEX_DEgenes_persample.R
14e5e3ebc5e4c2098dcba4d8d48757ef *R/GEX_GOterm.R
a975f0e78e218d760a131d85e3ddf0b5 *R/GEX_GSEA.R
b8f1d3041dc9fcec70248f1b3c747795 *R/GEX_automate.R
db5f5cd4d775d0c4c5ae4c28e2580d5b *R/GEX_clonotype.R
447f4b8c2b63df822a64a8e220d6a2fb *R/GEX_cluster_genes.R
950802c48732a325c4b66be9c961b71a *R/GEX_cluster_genes_heatmap.R
ec25eee9f3701c70554a6e9d6c41ede3 *R/GEX_cluster_membership.R
c299fc5426a5d99030988a9a99df2de8 *R/GEX_coexpression_coefficient.R
2c3f2a2ccbc071ce6611970c4e3d66f3 *R/GEX_dottile_plot.R
aa0915327198cf4414941a53606253d3 *R/GEX_heatmap.R
d991a38475c1899ff97bd7bdd6a8e94c *R/GEX_pairwise_degs.R
b635916d89727a7d141df5759bd4c148 *R/GEX_phenotype.R
07f2ee7827d9bb7814e973c3a44bd394 *R/GEX_phenotype_per_clone.R
9d779fbe8322213f3ddbff17de243fcc *R/GEX_proportions_barplot.R
90924f40c1078e0829a3281f9e4f58cc *R/GEX_scatter_coexpression.R
fa0b728954f838e9e465ab5781391bf8 *R/GEX_topN_DE_genes_per_cluster.R
66870e77130a597427819ab4d65ed7ca *R/GEX_visualize_clones.R
a36aca118c0da2c5681ff03ac5b2d2c6 *R/GEX_volcano.R
558469927f54a498448e6454ae004a18 *R/PlatypusDB_AIRR_to_VGM.R
9077be235faa3ff4ba9491e011012a0d *R/PlatypusDB_VGM_to_AIRR.R
7c60c88ce0ab840e3afdd6b47af0d4aa *R/PlatypusDB_fetch.R
a71587b8906d474b68175bcb97b4710b *R/PlatypusDB_find_CDR3s.R
8f296d003dee3278f4e3284f5342cf77 *R/PlatypusDB_list_projects.R
1658abe35acd8696d8237f2edc11bdcf *R/PlatypusDB_load_from_disk.R
bf3805e044a17682a149a394be9254ed *R/Platypus_data.R
1fe3c91d6ff46362154b5d8ac7c7e7e3 *R/VDJ_GEX_clonal_lineage_clusters.R
f9d310749bb50af922526890f1896afb *R/VDJ_GEX_clonotype_clusters_circos.R
6a3a269b70b1236ede1172ea9225657a *R/VDJ_GEX_expansion.R
3b4b29dca14bf3b7fb300cf4d0a0752f *R/VDJ_GEX_integrate.R
d5241a752179a39fb742751e7dbec603 *R/VDJ_GEX_matrix.R
d8c927574fd04f2ad57394834743f38c *R/VDJ_GEX_overlay_clones.R
1cdfb34235c0e0cf60e15b59499f0023 *R/VDJ_GEX_stats.R
e9ae2316fb95a37ede934a269b9a4154 *R/VDJ_VJ_usage_circos.R
f3c197e72dd31c13c746f7f1053b6eea *R/VDJ_Vgene_usage.R
875cb2edc68e958522b96989b44a677e *R/VDJ_Vgene_usage_barplot.R
561f8b101a1513adfb862809f32f2eac *R/VDJ_Vgene_usage_stacked_barplot.R
497b9561ebc97acac41ea5b432d91199 *R/VDJ_alpha_beta_Vgene_circos.R
d62e71272a5810fc126434362d3b6183 *R/VDJ_analyze.R
48b81e9423d076e37ce52e673034c785 *R/VDJ_assemble_for_PnP.R
5cf610437c7e8527fba89a93779e4ed7 *R/VDJ_call_MIXCR.R
2aeef06a0c488a3a8fd83aa3942ddfed *R/VDJ_circos.R
924af363a88305bf77cfc697068accc9 *R/VDJ_clonal_donut.R
09c546b5a60f9336bed903b08520e130 *R/VDJ_clonal_expansion.R
aa986fd8db43cdec0842fb0c42feb5e9 *R/VDJ_clonal_lineages.R
32f558fd2907b36ca4f3dfc3955180aa *R/VDJ_clonotype.R
299ff4ee838ed93eb768b679fd1afb87 *R/VDJ_contigs_to_vgm.R
5b915235f689aed5a0e43ea2f5ae7332 *R/VDJ_diversity.R
69aef29d150438bce42897dc71546d64 *R/VDJ_dublets.R
491a6b2553121b290070069f29c0fa42 *R/VDJ_extract_germline.R
fadee64e2606f4a1721e5a143bdbd2ba *R/VDJ_isotypes_per_clone.R
1041ec6d22094cb31874b2c343680348 *R/VDJ_logoplot_vector.R
10cea5d10c99140c57862f2ce43702c8 *R/VDJ_network.R
9fbdf8f192dbe1a8a267a46b53f3e717 *R/VDJ_overlap_heatmap.R
eddd36627bab37df12f969eabee92d60 *R/VDJ_per_clone.R
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c1824ad996769fb3941f2f26870115c2 *R/VDJ_reclonotype_list_arrange.R
b73e6873c3cdc3ba4146e6c6f9e2981f *R/VDJ_tree.R
9f35a495488f2d0bd8e896cebf13f71c *R/VDJ_variants_per_clone.R
9a3fc3a8f591b294a8116e3c13800a47 *R/automate_GEX.R
ea80b5f80c2dbd7e11cc9dec4f938f78 *R/call_MIXCR.R
777d9c074ba9fc94ff514eda21d65b80 *README.md
ed847007d66f6fe3c67ab0da4acd22da *build/vignette.rds
f4eba4baefcbe18824786649ce52d6c7 *data/ABForests_sysdata.rda
88c197db69c3d02f010253a42ade9419 *data/Bcell_sequences_example_tree.rda
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f42b87f1003ec4a887453efbe8480318 *data/class_switch_prob_hum.rda
f6268a6161c247af8ac25a43f5b49c74 *data/class_switch_prob_mus.rda
392685ab52dfe756b3f34f9f8086f1b7 *data/colors.rda
10ff2a61bb5169081dbd441f9c2e6747 *data/hotspot_df.rda
131e723ca1b0cae510ac807d9ce0442c *data/hum_b_h.rda
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867e3860f987f7eaae2b2b26a335fbb4 *data/iso_SHM_prob.rda
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95ff15d331134283860f660f5ad3727e *data/mus_b_trans.rda
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7d83c121c46482da5a31e66db6a5afff *data/mus_t_l.rda
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7f9532de8c48f9344f29039015988fe1 *data/trans_switch_prob_b.rda
173458f7a210df860e545ef614211368 *data/trans_switch_prob_t.rda
847bb9de266db1ac814af6833fddeefd *data/vdj_length_prob.rda
7cdf4c79d10fe243dbda4ba2ec51cb85 *inst/doc/PlatypusV3_agedCNS.R
790205cf751a7934bcfda0bec93318a1 *inst/doc/PlatypusV3_agedCNS.Rmd
6a1ec60c2c364cd11b9f27f89c21fa5c *inst/doc/PlatypusV3_agedCNS.html
60dec5acf6a50bf221995d4292eb3234 *man/AbForests_AntibodyForest.Rd
57684693711d86a7b8595e4fb3b8d409 *man/AbForests_CompareForests.Rd
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7add27e9966139ee2dd579d8efffc999 *man/AbForests_CsvToDf.Rd
26222b9aeb53a78c56b57f49f924c3e4 *man/AbForests_ForestMetrics.Rd
cd73f9971644274326793f5269a093f5 *man/AbForests_PlotGraphs.Rd
b2a6756bd620a074f57f1e3ace7d074e *man/AbForests_PlyloToMatrix.Rd
a6463349b2820dd60fd7c16a73dbe09f *man/AbForests_RemoveNets.Rd
2c677493a7ce96d2f65dc1a556e58263 *man/AbForests_SubRepertoiresByCells.Rd
a8367d4b3982bd7aba65792be0273f3b *man/AbForests_SubRepertoiresByUniqueSeq.Rd
9a16bb823507ded1b7dfb71ea8b7f7cb *man/AbForests_UniqueAntibodyVariants.Rd
854322bfa1ad66c06a01ac0aa705846c *man/Bcell_sequences_example_tree.Rd
25057dcf4652ebd79cbb881c593d6d2f *man/Bcell_tree_2.Rd
fc355d9e05a05a03525fba62ad33f955 *man/Echidna_vae_generate.Rd
b1235193bb0426a9171cb8fac3257ce0 *man/GEX_DEgenes.Rd
02664634f7a97ca2dd642ef391e6cf82 *man/GEX_DEgenes_persample.Rd
c0143ab3b1308fb0daa54055cf6a70b8 *man/GEX_GOterm.Rd
951f0006bb5e715350998226619d3329 *man/GEX_GSEA.Rd
914bdcb3191454fe771f93fe38369eca *man/GEX_automate.Rd
9bf19d7453aea4d477984a7036cf5a33 *man/GEX_clonotype.Rd
6e8b5110965bda6b3ba06f5cca9954f9 *man/GEX_cluster_genes.Rd
d8c3c872fc9b30481d65df79bd33c144 *man/GEX_cluster_genes_heatmap.Rd
ee2e7d4e20b5576de95d184c0c1d8361 *man/GEX_cluster_membership.Rd
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986baee1c656bd9aebf5e0490547a9bc *man/GEX_dottile_plot.Rd
4c3aa725093f8a1adca8c9d2f6610024 *man/GEX_heatmap.Rd
4065e9a7d2cde1203ee4dfb5485d4f4f *man/GEX_pairwise_DEGs.Rd
8ffcfa8f0f564288cccf6d07b1528520 *man/GEX_phenotype.Rd
22dc4f1ba5912126c52469fc833eb7f7 *man/GEX_phenotype_per_clone.Rd
09a8d6fdaa7fba01f7cc487fe78d83d7 *man/GEX_proportions_barplot.Rd
30502a60a4e6358bc6742d845f72b16b *man/GEX_scatter_coexpression.Rd
86a2108fc0cdc00b637e18152b71ce4c *man/GEX_topN_DE_genes_per_cluster.Rd
e29bb2b7facfaff7f7adabebaf95d43a *man/GEX_visualize_clones.Rd
d91d5f050dfec61f974a4aab5211a36a *man/GEX_volcano.Rd
14bcc3c8bf21c2d94a62fb89f26d8e83 *man/PlatypusDB_AIRR_to_VGM.Rd
3a517c7d418d0cae7ac21386edbd0c1e *man/PlatypusDB_VGM_to_AIRR.Rd
ff90cd5b3051f56b1117572741972646 *man/PlatypusDB_fetch.Rd
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014b354ba0011efe4d60b6da764cdf4a *man/PlatypusDB_load_from_disk.Rd
0304c10808237863cecfd196091676bd *man/VDJ_GEX_clonal_lineage_clusters.Rd
530f1feebba40f2b173d3bacf6128243 *man/VDJ_GEX_expansion.Rd
85abc6ad82629c9d48c1bdc2f805d33c *man/VDJ_GEX_integrate.Rd
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9eb83c9f5c0b23853b8ff480c07cc4c6 *man/VDJ_GEX_stats.Rd
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1b4de49c4004459ccfe2d91092e49f5a *man/VDJ_Vgene_usage.Rd
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1b6807f9eb526eac86890b4f06daedea *man/VDJ_analyze.Rd
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721f859504271e6abade052e01746047 *man/VDJ_call_MIXCR.Rd
413ba3393af7c9ee14dcc3f61ff3b472 *man/VDJ_circos.Rd
da18a7141b88b5517cd86e1d101addab *man/VDJ_clonal_donut.Rd
92712d3e1a94bf06efb46b5387decec7 *man/VDJ_clonal_expansion.Rd
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4a9b5b6b94f8d2bdc8464958816b054c *man/VDJ_clonotype.Rd
1d871bcb1cde2ae2ea4f32b719b0a93e *man/VDJ_clonotype_clusters_circos.Rd
9508fc4e12d962839c11a6eb77359c6b *man/VDJ_contigs_to_vgm.Rd
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fa675ae699fecfcd069ad8fd23191ee6 *man/VDJ_dublets.Rd
2027deb780216321f6ee27d8031e7da2 *man/VDJ_extract_germline.Rd
482374db01d066ba1515e884f1d78043 *man/VDJ_isotypes_per_clone.Rd
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59f8db0078de164c5915ed73be073599 *man/VDJ_per_clone.Rd
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2ec7ff2f871b8f67791826add229ee46 *man/automate_GEX.Rd
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2d5a3e049245448f1a5d5db0a709cbdf *man/mus_b_trans.Rd
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455ccdb6a5fdee83224efbcb91ccfe55 *man/small_vgm.Rd
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cad2cb5bd57edcb229ae92639b5573a6 *man/trans_switch_prob_b.Rd
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f242129d7b366213b5400f55c3fc6bc4 *man/vdj_length_prob.Rd
790205cf751a7934bcfda0bec93318a1 *vignettes/PlatypusV3_agedCNS.Rmd
