Files in currocam/FascinRSCA
R and Python code for SCA with fascin protein
.Rbuildignore
.gitignore
DESCRIPTION
FascinRSCA.Rproj
LICENSE.md
NAMESPACE
R/annotation_Uniprot_query.R
R/create_hmmer_json_dataframe.R
R/create_ncbi_basic_tax_dataframe.R
R/extractEMBOSS_StartEnd.R
R/extractEMBOSS_antigenic.R
R/extractEMBOSS_pepdigest.R
R/extractEMBOSS_tsv.R
R/multiple_fasta_files.R
R/outliers_boxplot_with_plotly.R
R/utils-pipe.R
README.Rmd
README.md
data-raw/df_Q16658.R
data-raw/df_Q16658/outliers_fasta_headers.txt
data-raw/df_Q16658_WithOutOutliers.R
data-raw/fasta_freezing_ann_hmmer/fascin.fasta
data-raw/fasta_freezing_ann_hmmer/fascin1.fasta
data-raw/fasta_freezing_ann_hmmer/fascin2.fasta
data-raw/fasta_freezing_ann_hmmer/fascin2a.fasta
data-raw/fasta_freezing_ann_hmmer/singed.fasta
data-raw/fasta_freezing_ann_hmmer/uncharacterized.fasta
data-raw/hmmer_Q16658.R
data-raw/hmmer_Q16658/2021_06_26-Q16658-Ensembl-fullseq.fa
data-raw/hmmer_Q16658/2021_06_26-Q16658-Ensembl.json
data-raw/hmmer_Q16658/2021_06_26-Q16658-Ensembl.tsv
data-raw/hmmer_Q16658/2021_06_26-Q16658-RefProteomes-fullseq.fa
data-raw/hmmer_Q16658/2021_06_26-Q16658-RefProteomes.json
data-raw/hmmer_Q16658/2021_06_26-Q16658-RefProteomes.tsv
data-raw/hmmer_Q16658/2021_06_26-Q16658-SwissProt-fullseq.fa
data-raw/hmmer_Q16658/2021_06_26-Q16658-SwissProt.json
data-raw/hmmer_Q16658/2021_06_26-Q16658-SwissProt.tsv
data-raw/pepstats_Q16658/EMBOSS/fascin_homologous_1_500.pepstats
data-raw/pepstats_Q16658/EMBOSS/fascin_homologous_1_860.csv
data-raw/pepstats_Q16658/EMBOSS/fascin_homologous_1_860.pepstats
data-raw/pepstats_Q16658/EMBOSS/fascin_homologous_501_860.pepstats
data-raw/pepstats_Q16658/EMBOSS/parser_pepstats.py
data-raw/pepstats_Q16658/fascin_homologous_1_500.fasta
data-raw/pepstats_Q16658/fascin_homologous_501_860.fasta
data-raw/pepstats_Q16658/id_pepstats.txt
data/df_Q16658.rda
data/df_Q16658_WithOutOutliers.rda
data/freezing.rda
data/freezing_cluster.rda
data/hmmer_Q16658.rda
inst/README.md
inst/extdata/external/POSA/act/1dfcA-tran.pdb
inst/extdata/external/POSA/act/3llpA-tran.pdb
inst/extdata/external/POSA/low_act/3llpB-tran.pdb
inst/extdata/external/POSA/low_act/3p53A-tran.pdb
inst/extdata/external/POSA/low_act/4govA-tran.pdb
inst/extdata/external/POSA/low_act/4goyA-tran.pdb
inst/extdata/external/POSA/low_act/4gp0A-tran.pdb
inst/extdata/external/POSA/low_act/4gp3A-tran.pdb
inst/extdata/external/POSA/low_act/6b0tA-tran.pdb
inst/extdata/external/POSA/low_act/6i0zA-tran.pdb
inst/extdata/external/POSA/low_act/6i18A-tran.pdb
inst/extdata/external/accurate_ann/cluster_1_Arthropoda.result.aln
inst/extdata/external/accurate_ann/cluster_1_Arthropoda.result.dnd
inst/extdata/external/accurate_ann/cluster_1_Arthropoda.result.fa
inst/extdata/external/accurate_ann/cluster_1_Arthropoda.result.html
inst/extdata/external/accurate_ann/cluster_2_Chordata.result.aln
inst/extdata/external/accurate_ann/cluster_2_Chordata.result.dnd
inst/extdata/external/accurate_ann/cluster_2_Chordata.result.fa
inst/extdata/external/accurate_ann/cluster_2_Chordata.result.html
inst/extdata/external/accurate_ann/fascin_2_Chordata.result.aln
inst/extdata/external/accurate_ann/fascin_2_Chordata.result.dnd
inst/extdata/external/accurate_ann/fascin_2_Chordata.result.fa
inst/extdata/external/accurate_ann/fascin_2_Chordata.result.html
inst/extdata/external/structures_files/O14926-1/AF-O14926-F1-model_v2.pdb
inst/extdata/external/structures_files/fascin1/3p53_clean.pdb
inst/extdata/interim/EMBOSS_classifier_desc/NonRedundant_FSCN_Human_Homologous.fasta
inst/extdata/interim/EMBOSS_classifier_desc/NonRedundant_FSCN_Human_Homologous_edited.fasta
inst/extdata/interim/EMBOSS_classifier_desc/antigenic.tsv
inst/extdata/interim/EMBOSS_classifier_desc/antigenic_example.tsv
inst/extdata/interim/EMBOSS_classifier_desc/emboss_001.sig
inst/extdata/interim/EMBOSS_classifier_desc/proteolytic_Trypsin.tsv
inst/extdata/interim/fascin1_trim_hmm/align/hmmer_search.aln
inst/extdata/interim/fascin1_trim_hmm/align/hmmer_search.fullseq.fasta
inst/extdata/interim/fascin1_trim_hmm/align/hmmer_search_clustal.aln
inst/extdata/interim/fascin1_trim_hmm/fascin1.desc
inst/extdata/interim/fascin1_trim_hmm/fascin1.hmm
inst/extdata/interim/fascin1_trim_hmm/fascin1.trim.fasta_aln
inst/extdata/interim/fascin1_trim_hmm/fascin1.trim.fasta_aln.decoded
inst/extdata/interim/fascin1_trim_hmm/search/ensembl.fa
inst/extdata/interim/fascin1_trim_hmm/search/ensembl.json
inst/extdata/interim/fascin1_trim_hmm/search/ensembl.tsv
inst/extdata/interim/fascin1_trim_hmm/search/swissprot.aln
inst/extdata/interim/fascin1_trim_hmm/search/swissprot.fa
inst/extdata/interim/fascin1_trim_hmm/search/swissprot.json
inst/extdata/interim/fascin1_trim_hmm/search/swissprot.tsv
inst/extdata/interim/fascin1_trim_hmm/search/uniprotrefprot.fa
inst/extdata/interim/fascin1_trim_hmm/search/uniprotrefprot.json
inst/extdata/interim/fascin1_trim_hmm/search/uniprotrefprot.tsv
inst/extdata/interim/fascin1_trim_t_coffee/fascin1.fasta
inst/extdata/interim/fascin1_trim_t_coffee/fascin1.trim.code_name
inst/extdata/interim/fascin1_trim_t_coffee/fascin1.trim.coded.fasta
inst/extdata/interim/fascin1_trim_t_coffee/fascin1.trim.fasta
inst/extdata/interim/fascin1_trim_t_coffee/fascin1.trim.fasta_aln
inst/extdata/interim/fascin1_trim_t_coffee/result.aln
inst/extdata/interim/fascin1_trim_t_coffee/result.clustalw_aln
inst/extdata/interim/fascin1_trim_t_coffee/result.clustalw_aln.decoded
inst/extdata/interim/fascin1_trim_t_coffee/result.score_html.html
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier.txt
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_001_568.fasta
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_001_568_antigenic.tsv
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_001_568_pepdigest.tsv
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_001_568_pepstats.csv
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_001_568_sigcleave.tsv
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_1_500.fasta
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_1_500.pepstats
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_1_568.pepstats
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_501_568.fasta
inst/extdata/interim/fascin_ann_classifier_desc/fascinClassifier_501_568.pepstats
inst/extdata/interim/fascin_ann_classifier_desc/parser_pepstats.py
inst/extdata/interim/fascins_trim_hmm/hmmbuild/fascins.desc
inst/extdata/interim/fascins_trim_hmm/hmmbuild/fascins.hmm
inst/extdata/interim/fascins_trim_t_coffee/fascins.trim.code_name
inst/extdata/interim/fascins_trim_t_coffee/fascins.trim.coded.fasta
inst/extdata/interim/fascins_trim_t_coffee/fascins.trim.coded.fasta_aln
inst/extdata/interim/fascins_trim_t_coffee/fascins.trim.fasta
inst/extdata/interim/fascins_trim_t_coffee/fascins.trim.fasta_aln
inst/extdata/interim/gpad_fascin_rel_shared_GoAnn/QuickGO-1.gpad
inst/extdata/interim/gpad_fascin_rel_shared_GoAnn/QuickGO-2.gpad
inst/extdata/interim/gpad_fascin_rel_shared_GoAnn/QuickGO-3.gpad
inst/extdata/interim/gpad_fascin_rel_shared_GoAnn/QuickGO-4.gpad
inst/extdata/interim/gpad_fascin_rel_shared_GoAnn/README.md
inst/extdata/interim/negative_control/NonRelated.fasta
inst/extdata/interim/negative_control/RelateddbID.txt
inst/extdata/interim/negative_control/related_fascin.fasta
inst/extdata/processed/fascin1_hmmer_aln/hmmer_search.aln
inst/extdata/processed/fascin_ann_classifier_desc_prepro/.ipynb_checkpoints/Untitled-checkpoint.ipynb
inst/extdata/processed/fascin_ann_classifier_desc_prepro/FSCN1_Vs_others.csv
inst/extdata/processed/fascin_ann_classifier_desc_prepro/FSCN1_Vs_others_and_neg.csv
inst/extdata/processed/fascin_ann_classifier_desc_prepro/FSCN_rel_Vs_NonFSCN.csv
inst/extdata/processed/fascin_ann_classifier_desc_prepro/multiclasificador.csv
inst/extdata/processed/freezing_cluster_ann/freezing_fascin.csv
inst/extdata/processed/freezing_cluster_ann/peces_fascin.csv
inst/extdata/processed/structures_files/AlphaFold2/O14926-2/O14926_AlphaFold2.pdb
inst/extdata/processed/structures_files/AlphaFold2/O14926-2/predicted_aligned_error.json
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/O14926-2_RoseTTAFold.pdb
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/msa.a3m
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/msa_coverage.png
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/plddt.png
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/pred.npz
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/pred.scwrl.pdb
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/pred_init.pdb
inst/extdata/processed/structures_files/RoseTTAFold/O14926-2/settings.txt
man/annotation_uniprot_query.Rd
man/create_hmmer_json_dataframe.Rd
man/create_ncbi_basic_tax_dataframe.Rd
man/extractEMBOSS_StartEnd.Rd
man/extractEMBOSS_antigenic.Rd
man/extractEMBOSS_pepdigest.Rd
man/extractEMBOSS_tsv.Rd
man/multiple_fasta_files.Rd
man/outliers_boxplot_with_plotly.Rd
man/pipe.Rd
notebooks/01-currocam-Preparing_datasets.Rmd
notebooks/02-currocam-Exploratory_analysis_and_remove_outliers.Rmd
notebooks/03-currocam-FSCN1_Vs_FSCN2.Rmd
notebooks/04-currocam_CdelVal-PCA_fascin_freezing.Rmd
notebooks/05-currocam_clustering_fascin.Rmd
notebooks/06-currocam_alignments.Rmd
notebooks/07-currocam_balancear_clases.Rmd
notebooks/07-currocam_caret.Rmd
notebooks/07-currocam_protr_descriptors.Rmd
notebooks/07-currocam_protr_descriptors.html
notebooks/08-currocam_bior3d.Rmd
notebooks/POSA_bio3d.Rmd
notebooks/POSA_bio3d.html
notebooks/currocam-structural_FSCN1.Rmd
notebooks/currocam-structural_FSCN1.pdf
notebooks/currocam_hmmer.Rmd
notebooks/htmls/02-currocam-Exploratory_analysis_and_remove_outliers.html
notebooks/htmls/03-currocam-FSCN1_Vs_FSCN2.html
notebooks/htmls/04-currocam_CdelVal-PCA_fascin_freezing.html
notebooks/htmls/05-currocam_clustering_fascin.html
notebooks/htmls/07-currocam_balancear_clases.html
notebooks/htmls/07-currocam_protr_descriptors.html
notebooks/htmls/08-currocam_bior3d.html
notebooks/htmls/currocam_hmmer.html
tests/testthat.R
tests/testthat/emboss/antigenicExample.tsv
tests/testthat/hmmer_json.json
tests/testthat/test-annotation_uniprot_query.R
tests/testthat/test-create_hmmer_json_dataframe.R
tests/testthat/test-create_ncbi_basic_tax_dataframe.R
