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.gitignore
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.DS_Store
TGNE/microarray_QC/*.xys
TGNE/microarray_QC/pd.*
TGNE/microarray_QC/*.csv
*.Rhistory
*.ht2
*.html
*.sam
*.fna
*.ndf
TGNE/eggnog/*.csv
TGNE/embedding/test_nn3_leiden_label_df_round_1*.csv
TGNE/enrichment/test_nn3_full_enrichment.csv
TGNE/microarray_probe_alignment_and_filtering/*rma_expression*.csv
*.pkl
.RData
TGNE/embedding/mcl_rcl/TAG/*
TGNE/embedding/mcl_rcl_res*.csv
TGNE/embedding/mcl_rcl/mcl_rcl_res*.csv
TGNE/embedding/mcl_rcl/pfx*
TGNE/embedding/mcl_rcl/*.pdf
TGNE/embedding/mcl_rcl/*.mci
TGNE/embedding/mcl_rcl/*.tab
TGNE/embedding/mcl_rcl/*.txt
*.labels
*.RDataTmp
*.html.zip
.vscode/*
archived_pipelines/*
# TGNE/clustering_optimization/**/*.csv
*.db
TGNE/embedding/same_cluster_TTHERMS.txt
*.mci
TGNE/enrichment/*.csv
TGNE/eggnog/hmmer/*
TGNE/eggnog/pfam/*
TGNE/embedding/*.csv
TGNE/embedding/colors_1000_1
TGNE/embedding/colors_2000_1
*.annotations
*.pyc
active_files/*
*.gz
TGNE/enrichment/**/*.csv
*.zip
*.sbatch
!TGNE/clustering_optimization/*.sbatch
*.numbers
/curated_clusters/*
TGNE/embedding/layout_playground.ipynb
webgl_test.ipynb
*-checkpoint.ipynb
*.nbconvert.ipynb
new_raw_data/**/*.txt
new_raw_data/**/*.tar
new_raw_data/**/*.out
new_raw_data/**/*.csv
new_raw_data/**/*.tsv
new_raw_data/**/*.h5
new_raw_data/**/*.xls
new_raw_data/**/*.xlxs
new_raw_data/**/*.log
new_raw_data/**/*.gff3
new_raw_data/**/*.fasta
new_raw_data/all_pair/**/*
/TGNE/microarray_probe_alignment_and_filtering/hisat2-2.2.1
TGNE/embedding/emine_ttherms.txt
TGNE/interproscan/**/*.tsv
TGNE/interproscan/**/*.csv
**/archive/*
input_data/eggnog_annotations_file
input_data/genome_model
input_data/interproscan_tsv_file
TGNE/clustering_optimization/*_clr_for_distances_*nn.Rmd
*.svg
regranulation/**/*.fasta
regranulation/**/*.pdf
regranulation/**/*.doc
regranulation/**/*.xlsx
regranulation/**/*.csv
regranulation/hisat2*/**/*
regranulation/Microarray raw data/*
/regranulation/pd.tetexpr/**/*
new_raw_data/rna_seq_processed/**/*
new_raw_data/tgd2024/**/*
new_raw_data/*.ipynb
TGNE/embedding/*.txt
TGNE/embedding/*.Rmd
TGNE/embedding/*.sh
TGNE/embedding/*.py
/regranulation/pd.filtered.tetexpr
/regranulation/raw_data