Files in MaudeDavidLab/gut_microbiome_embeddings_package
Creates a Matrix of Embeddings
.gitattributes
DESCRIPTION
GMEmbeddings.Rproj
LICENSE
NAMESPACE
R/embed_asv_table_new.R
R/getEmbeddingMatrix.R
R/getGenePathwayTableKegg.R
R/making_embedding_transformation_matrix/DADA2_pipeline.R
R/making_embedding_transformation_matrix/filterASVs.py
R/making_embedding_transformation_matrix/filter_blast_hits.sh
R/making_embedding_transformation_matrix/make_GloVe_input.py
R/making_embedding_transformation_matrix/make_PCA_transformation_matrix.py
R/making_embedding_transformation_matrix/making_embedding_transformation_matrix.md
README.md
embed_example.Rmd
inst/extdata/.gitattributes
inst/extdata/glove_transformation_matrices/.gitattributes
inst/extdata/glove_transformation_matrices/glove_emb_fullseq_100.txt
inst/extdata/glove_transformation_matrices/glove_emb_fullseq_250.txt
inst/extdata/glove_transformation_matrices/glove_emb_fullseq_50.txt
inst/extdata/glove_transformation_matrices/glove_emb_id_100.txt
inst/extdata/glove_transformation_matrices/glove_emb_id_250.txt
inst/extdata/glove_transformation_matrices/glove_emb_id_50.txt
inst/extdata/pathways/asv_by_pathway.rds
inst/extdata/pca_transformation_matrices/pca_transformation_matrix_250.csv
inst/extdata/pca_transformation_matrices/pca_transformation_matrix_ids_100.csv
inst/extdata/pca_transformation_matrices/pca_transformation_matrix_ids_250.csv
inst/extdata/pca_transformation_matrices/pca_transformation_matrix_ids_50.csv
inst/extdata/test_dataset_1/asv_table.csv
inst/extdata/test_dataset_1/best_hits.tsv
inst/extdata/test_dataset_1/repseqs.fasta
inst/extdata/test_datasets/num_seqs_aligned_baxter.csv
inst/extdata/test_datasets/num_seqs_aligned_halfvarson.csv
inst/extdata/test_datasets/num_seqs_aligned_m3.csv
inst/extdata/test_datasets/num_seqs_aligned_pilot.csv
inst/extdata/test_datasets/num_seqs_aligned_schirmer.csv
inst/extdata/test_datasets/num_seqs_aligned_zeller.csv
inst/extdata/test_datasets/percent_seqs_aligned_baxter.csv
inst/extdata/test_datasets/percent_seqs_aligned_halfvarson.csv
inst/extdata/test_datasets/percent_seqs_aligned_m3.csv
inst/extdata/test_datasets/percent_seqs_aligned_pilot.csv
inst/extdata/test_datasets/percent_seqs_aligned_schirmer.csv
inst/extdata/test_datasets/percent_seqs_aligned_zeller.csv
man/embed_asv_table_new.Rd
man/files_to_cutadapt_round1.sh
man/files_to_cutadapt_round2.sh
man/filterLargeFiles.sh
man/getBlastHits.Rd
man/getEmbeddingMatrix.Rd
man/getFasta.Rd
man/getSeqtab.Rd
