Files in brouwern/compbio4all
Datasets and helpful functions for learning bioinformatics and computational biology
.DS_Store
.Rbuildignore
.Rhistory
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/.DS_Store
R/.Rhistory
R/AOU_species_codes.R
R/BBS_PA.R
R/BBS_PA_SCTA.R
R/BBS_PA_combo_cover_1km.R
R/BBS_PA_landcover_1km.R
R/NA_to_zero.R
R/aa_chars.R
R/aa_chars_subset.R
R/aa_dat.R
R/antlers.R
R/blastr.R
R/brook_trout.R
R/brook_trout_ABD.R
R/chargaff1951.R
R/clean_alignment.R
R/combine_NLCD_classes.R
R/compbio4all-package.R
R/dengue_seq_1_2_3_4.R
R/dengue_seq_1_2_3_4_stringset.R
R/dengueseq_fasta.R
R/dengueseqstartstring.R
R/diag_show.R
R/dmshrm_blast_1.R
R/dmshrm_blast_2.R
R/dna_seq_stringset.R
R/doves_PA.R
R/doves_PA_3_years.R
R/eaglesOH.R
R/eaglesPA.R
R/eaglesWV.R
R/eggs.R
R/eggs_and_nests.R
R/eggs_and_nests2.R
R/ensemblleshmania.R
R/ensemblpfalciparum.R
R/entrez_fetch_list.R
R/expand_BBS_routes.R
R/fasta_cleaner.R
R/find_ORFs_in_seq.R
R/find_start_stop_codons.R
R/frogarms.R
R/generate_hmm_seq.R
R/generate_markov_seq.R
R/genes_dpc.R
R/genes_hpc.R
R/genes_mpc.R
R/hShroom2.R
R/hShroom3.R
R/human_bodytemp.R
R/human_gene_lengths.R
R/leishmaniagenes.R
R/leishmaniagenes2.R
R/mShroom3a.R
R/make_dataset_helpfile.R
R/make_my_data2L.R
R/make_seqs_multinom_mod.R
R/make_viterbi_mat.R
R/martin1995.R
R/milk.R
R/pams.R
R/pfalciparumgenes.R
R/pikas.R
R/plot_ORFs_in_seq.R
R/plot_sliding_window.R
R/plot_starts_and_stops.R
R/print_msa.R
R/print_pairwise_alignment.R
R/robinson_aafreq.R
R/rooted_NJ_tree.R
R/sShroom.R
R/sample_BBS_routes.R
R/sample_dove_routes.R
R/score_alignment.R
R/shroom_table.R
R/tri_print.R
R/trillium.R
R/virus_mrna_aln.R
R/virus_mrna_aln_bin.R
R/virus_mrna_dist.R
R/virus_snc.R
R/virus_snr.R
R/virusaln.R
R/virusaln_seqinr.R
R/virusaln_seqinr_clean.R
R/viterbi.R
R/wetlands.R
R/wine.R
R/woodcock_MI_3_years.R
README.md
_pkgdown.yml
compbio4all.Rproj
data-raw/.DS_Store
data-raw/DATASET.R
data-raw/Higgs_2009_amino_acids_properties.csv
data-raw/doves_PA.csv
data-raw/download_shroom_seqs.R
data-raw/gene_length_danio_protein_coding.csv
data-raw/gene_length_human_protein_coding.csv
data-raw/gene_length_mus_protein_coding.csv
data-raw/mRNA_initiation.csv
data-raw/make_Higgs2009_data.R
data-raw/make_chargaff1951.R
data-raw/make_chargaff1969.R
data-raw/make_dengue_seq_msa_files.R
data-raw/make_dengueseq_fasta.R
data-raw/make_dengueseqstartstring.R
data-raw/make_dshrm_blast_x.R
data-raw/make_ensemble_x.R
data-raw/make_gene_lengths_dpc.R
data-raw/make_gene_lengths_hpc.R
data-raw/make_gene_lengths_mpc.R
data-raw/make_mRNA_initiation.R
data-raw/make_martin1995_life_history.R
data-raw/make_robinson.R
data-raw/make_robinson_aa.R
data-raw/make_shroom_table.R
data-raw/make_virus_mutation_rates.R
data-raw/make_wine.R
data-raw/martin1995_life_history.csv
data-raw/pan.fasta
data-raw/pan.txt
data-raw/pan_align.aux
data-raw/pan_align.log
data-raw/pan_align.pdf
data-raw/pan_align.tex
data-raw/pevsner3.csv
data-raw/pevsner3.pdf
data-raw/pevsner3_fig3_13.csv
data-raw/pevsner3_fig3_14.csv
data-raw/pevsner3_fig3_15.csv
data-raw/pevsner3_fig3_8.csv
data-raw/pevsner3_fig3_9.csv
data-raw/pevsner_ch3_dayoff_martices.R
data-raw/phosphoproteins.fasta
data-raw/pikas.xlsx
data-raw/prep_antlers.R
data-raw/prep_faaborg.R
data-raw/prep_trillium_PLE.Rmd
data-raw/robinson_aafreq.csv
data-raw/set_up_doves.Rmd
data-raw/set_up_pika.Rmd
data-raw/shrooms.txt
data-raw/shrooms_align.pdf
data-raw/shrooms_align.tex
data-raw/virus_mutation_rates_snc.csv
data-raw/virus_mutation_rates_snr.csv
data/.DS_Store
data/AOU_species_codes.RData
data/BBS_PA.RData
data/BBS_PA_SCTA.RData
data/BBS_PA_combo_cover_1km.RData
data/BBS_PA_landcover_1km.RData
data/aa_chars.rda
data/aa_chars_subset.rda
data/aa_dat.rda
data/antlers.RData
data/brook_trout.RData
data/brook_trout_ABD.RData
data/chargaff1951.rda
data/dengueseq_fasta.rda
data/dengueseqstartstring.rda
data/dmshrm_blast_1.rda
data/dmshrm_blast_2.rda
data/dna_seq_stringset.rda
data/doves_PA.RData
data/doves_PA_3_years.RData
data/eaglesOH.RData
data/eaglesPA.RData
data/eaglesWV.RData
data/eggs.RData
data/eggs_and_nests.RData
data/eggs_and_nests2.RData
data/ensemblleishmania.rda
data/ensemblpfalciparum.rda
data/frogarms.RData
data/genes_dpc.rda
data/genes_hpc.rda
data/genes_mpc.rda
data/hShroom2.rda
data/hShroom3.rda
data/human_bodytemp.RData
data/human_gene_lengths.rda
data/leishmaniagenes.rda
data/leishmaniagenes2.rda
data/mShroom3a.rda
data/martin1995.rda
data/milk.RData
data/pams.rda
data/pfalciparumgenes.rda
data/pikas.RData
data/robinson_aafreq.rda
data/sShroom.rda
data/seq_1_2_3_4.rda
data/seq_1_2_3_4_stringset.rda
data/shroom_table.rda
data/trillium.RData
data/virus_mrna_aln.rda
data/virus_mrna_aln_bin.rda
data/virus_mrna_dist.rda
data/virus_snc.rda
data/virus_snr.rda
data/virusaln.rda
data/virusaln_seqinr.rda
data/virusaln_seqinr_clean.rda
data/wetlands.RData
data/wine.rda
data/woodcock_MI_3_years.RData
docs/404.html
docs/LICENSE.html
docs/articles/index.html
docs/articles/zzz1-temp.html
docs/articles/zzz1-temp_files/header-attrs-2.10/header-attrs.js
docs/articles/zzz3-creating_this_package.html
docs/articles/zzz3-creating_this_package_files/header-attrs-2.10/header-attrs.js
docs/articles/zzz4-document_datasets.html
docs/articles/zzz4-document_datasets_files/header-attrs-2.10/header-attrs.js
docs/articles/zzz5-build_and_rebuild_package.html
docs/articles/zzz5-build_and_rebuild_package_files/header-attrs-2.10/header-attrs.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/AOU_species_codes.html
docs/reference/BBS_PA.html
docs/reference/BBS_PA_SCTA.html
docs/reference/BBS_PA_combo_cover_1km.html
docs/reference/BBS_PA_landcover_1km.html
docs/reference/NA_to_zero.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/aa_chars.html
docs/reference/aa_chars_subset.html
docs/reference/aa_dat.html
docs/reference/antlers.html
docs/reference/blastr.html
docs/reference/brook_trout.html
docs/reference/brook_trout_ABD.html
docs/reference/chargaff1951.html
docs/reference/clean_alignment.html
docs/reference/combine_NLCD_classes.html
docs/reference/compbio4all-package.html
docs/reference/dengueseq_fasta.html
docs/reference/dengueseqstartstring.html
docs/reference/diag_show.html
docs/reference/dmshrm_blast_1.html
docs/reference/dmshrm_blast_2.html
docs/reference/dna_seq_stringset.html
docs/reference/doves_PA.html
docs/reference/doves_PA_3_years.html
docs/reference/eaglesOH-1.png
docs/reference/eaglesOH.html
docs/reference/eaglesPA-1.png
docs/reference/eaglesPA.html
docs/reference/eaglesWV-1.png
docs/reference/eaglesWV.html
docs/reference/eggs-1.png
docs/reference/eggs.html
docs/reference/eggs_and_nests.html
docs/reference/eggs_and_nests2-1.png
docs/reference/eggs_and_nests2.html
docs/reference/ensemblleishmania.html
docs/reference/ensemblpfalciparum.html
docs/reference/entrez_fetch_list.html
docs/reference/expand_BBS_routes.html
docs/reference/fasta_cleaner.html
docs/reference/find_ORFs_in_seq.html
docs/reference/find_start_stop_codons.html
docs/reference/frogarms-1.png
docs/reference/frogarms-2.png
docs/reference/frogarms.html
docs/reference/generate_hmm_seq.html
docs/reference/generate_markov_seq.html
docs/reference/genes_dpc.html
docs/reference/genes_hpc.html
docs/reference/genes_mpc.html
docs/reference/hShroom2.html
docs/reference/hShroom3.html
docs/reference/human_bodytemp-1.png
docs/reference/human_bodytemp.html
docs/reference/human_gene_lengths.html
docs/reference/index.html
docs/reference/leishmaniagenes.html
docs/reference/leishmaniagenes2.html
docs/reference/mShroom3a.html
docs/reference/make_dateset_helpfile.html
docs/reference/make_my_data2L.html
docs/reference/make_seqs_multinom_mod.html
docs/reference/make_viterbi_mat.html
docs/reference/martin1995.html
docs/reference/milk.html
docs/reference/pams.html
docs/reference/pfalciparumgenes.html
docs/reference/pikas-1.png
docs/reference/pikas-2.png
docs/reference/pikas-3.png
docs/reference/pikas-4.png
docs/reference/pikas.html
docs/reference/plot_ORFs_in_seq-1.png
docs/reference/plot_ORFs_in_seq-2.png
docs/reference/plot_ORFs_in_seq.html
docs/reference/plot_sliding_window.html
docs/reference/plot_start_stop_codons-1.png
docs/reference/plot_start_stop_codons-2.png
docs/reference/plot_start_stop_codons.html
docs/reference/print_msa.html
docs/reference/print_pairwise_alignment.html
docs/reference/robinson_aafreq.html
docs/reference/rooted_NJ_tree.html
docs/reference/sShroom.html
docs/reference/sample_BBS_routes.html
docs/reference/sample_dove_routes.html
docs/reference/score_alignment.html
docs/reference/seq_1_2_3_4.html
docs/reference/seq_1_2_3_4_stringset.html
docs/reference/shroom_table.html
docs/reference/tri_print.html
docs/reference/trillium.html
docs/reference/virus_mrna_aln.html
docs/reference/virus_mrna_aln_bin.html
docs/reference/virus_mrna_dist.html
docs/reference/virus_snc.html
docs/reference/virus_snr.html
docs/reference/virusaln.html
docs/reference/virusaln_seqinr.html
docs/reference/virusaln_seqinr_clean.html
docs/reference/viterbi.html
docs/reference/wetlands.html
docs/reference/wine.html
docs/reference/woodcock_MI_3_years-1.png
docs/reference/woodcock_MI_3_years.html
inst/.DS_Store
inst/extdata/.DS_Store
inst/extdata/A0PQ23.fasta
inst/extdata/Q9CD83.fasta
inst/extdata/aa_chars_subset
inst/extdata/aa_chars_subset.dat
inst/extdata/dengueseq.fasta
man/AOU_species_codes.Rd
man/BBS_PA.Rd
man/BBS_PA_SCTA.Rd
man/BBS_PA_combo_cover_1km.Rd
man/BBS_PA_landcover_1km.Rd
man/NA_to_zero.Rd
man/aa_chars.Rd
man/aa_chars_subset.Rd
man/aa_dat.Rd
man/antlers.Rd
man/blastr.Rd
man/brook_trout.Rd
man/brook_trout_ABD.Rd
man/chargaff1951.Rd
man/clean_alignment.Rd
man/combine_NLCD_classes.Rd
man/compbio4all-package.Rd
man/dengueseq_fasta.Rd
man/dengueseqstartstring.Rd
man/diag_show.Rd
man/dmshrm_blast_1.Rd
man/dmshrm_blast_2.Rd
man/dna_seq_stringset.Rd
man/doves_PA.Rd
man/doves_PA_3_years.Rd
man/eaglesOH.Rd
man/eaglesPA.Rd
man/eaglesWV.Rd
man/eggs.Rd
man/eggs_and_nests.Rd
man/eggs_and_nests2.Rd
man/ensemblleishmania.Rd
man/ensemblpfalciparum.Rd
man/entrez_fetch_list.Rd
man/expand_BBS_routes.Rd
man/fasta_cleaner.Rd
man/find_ORFs_in_seq.Rd
man/find_start_stop_codons.Rd
man/frogarms.Rd
man/generate_hmm_seq.Rd
man/generate_markov_seq.Rd
man/genes_dpc.Rd
man/genes_hpc.Rd
man/genes_mpc.Rd
man/hShroom2.Rd
man/hShroom3.Rd
man/human_bodytemp.Rd
man/human_gene_lengths.Rd
man/leishmaniagenes.Rd
man/leishmaniagenes2.Rd
man/mShroom3a.Rd
man/make_dateset_helpfile.Rd
man/make_my_data2L.Rd
man/make_seqs_multinom_mod.Rd
man/make_viterbi_mat.Rd
man/martin1995.Rd
man/milk.Rd
man/pams.Rd
man/pfalciparumgenes.Rd
man/pikas.Rd
man/plot_ORFs_in_seq.Rd
man/plot_sliding_window.Rd
man/plot_start_stop_codons.Rd
man/print_msa.Rd
man/print_pairwise_alignment.Rd
man/robinson_aafreq.Rd
man/rooted_NJ_tree.Rd
man/sShroom.Rd
man/sample_BBS_routes.Rd
man/sample_dove_routes.Rd
man/score_alignment.Rd
man/seq_1_2_3_4.Rd
man/seq_1_2_3_4_stringset.Rd
man/shroom_table.Rd
man/tri_print.Rd
man/trillium.Rd
man/virus_mrna_aln.Rd
man/virus_mrna_aln_bin.Rd
man/virus_mrna_dist.Rd
man/virus_snc.Rd
man/virus_snr.Rd
man/virusaln.Rd
man/virusaln_seqinr.Rd
man/virusaln_seqinr_clean.Rd
man/viterbi.Rd
man/wetlands.Rd
man/wine.Rd
man/woodcock_MI_3_years.Rd
vignettes/.DS_Store
vignettes/.gitignore
vignettes/zzz1-temp.Rmd
vignettes/zzz3-creating_this_package.Rmd
vignettes/zzz4-document_datasets.Rmd
vignettes/zzz5-build_and_rebuild_package.Rmd
