GitHub - JudoWill/flELM: A project to find the source-organism of a flu sequence based on the specificity of functional sites.

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A project to find the source-organism of a flu sequence based on the specificity of functional sites.

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Name		Name	Last commit message	Last commit date
Latest commit History 217 Commits
papers		papers
.gitignore		.gitignore
README		README
biomart_submit.py		biomart_submit.py
check.py		check.py
check_host_aa_freqs.py		check_host_aa_freqs.py
clean_elms.py		clean_elms.py
cluster_elmSeqs.py		cluster_elmSeqs.py
cmp_flu_elms.py		cmp_flu_elms.py
combine_elmdicts.py		combine_elmdicts.py
convert_elm_hits.py		convert_elm_hits.py
cor.py		cor.py
cos_elmCount_host_dis_redo.py		cos_elmCount_host_dis_redo.py
cos_elmFreq_host_dis_dendrogram.py		cos_elmFreq_host_dis_dendrogram.py
cos_elmSeqFreq_host_dis.py		cos_elmSeqFreq_host_dis.py
cos_host_host.py		cos_host_host.py
cos_host_host_sums.py		cos_host_host_sums.py
cos_host_virus.py		cos_host_virus.py
count_flu.py		count_flu.py
count_flu_seqs.py		count_flu_seqs.py
count_hprd.py		count_hprd.py
count_missing_seqs.py		count_missing_seqs.py
doVirusELMseqsHaveLowHostFreqs.py		doVirusELMseqsHaveLowHostFreqs.py
elm_expressions.clean		elm_expressions.clean
elm_hists.py		elm_hists.py
elm_seqCount_hist.py		elm_seqCount_hist.py
elm_seq_hits_hist.py		elm_seq_hits_hist.py
euc_elmFreq_host.py		euc_elmFreq_host.py
exp_fraction.py		exp_fraction.py
findGoodProteins.py		findGoodProteins.py
find_diffs.py		find_diffs.py
find_diffs_2.py		find_diffs_2.py
find_diffs_3.py		find_diffs_3.py
find_diffs_4.py		find_diffs_4.py
find_good_phylogeny_elms.py		find_good_phylogeny_elms.py
flu_project_host_flu_closest.py		flu_project_host_flu_closest.py
funcs.R		funcs.R
getConserved.py		getConserved.py
getConservedELMseqs.py		getConservedELMseqs.py
getDiffSeqsForDiffVirusELMs.py		getDiffSeqsForDiffVirusELMs.py
getELMfreq.py		getELMfreq.py
getEntropy.py		getEntropy.py
getSeqFrac.py		getSeqFrac.py
get_aa_freq.py		get_aa_freq.py
get_bird_elms.py		get_bird_elms.py
get_cons_elms.py		get_cons_elms.py
get_diAA_freq.py		get_diAA_freq.py
get_elm_patterns.py		get_elm_patterns.py
get_ensembl_monkey_protein_seqs.py		get_ensembl_monkey_protein_seqs.py
get_ensembl_protein_seqs.py		get_ensembl_protein_seqs.py
get_flu_aa_freq.py		get_flu_aa_freq.py
get_flu_seqs.py		get_flu_seqs.py
get_host_elms.py		get_host_elms.py
get_mammal_bird_diffs.py		get_mammal_bird_diffs.py
get_protein_seq_for_gi.py		get_protein_seq_for_gi.py
get_ratios.py		get_ratios.py
get_single_clusters.py		get_single_clusters.py
get_uniq_flu.py		get_uniq_flu.py
global_settings.py		global_settings.py
heat.py		heat.py
heat_flu_proteins.py		heat_flu_proteins.py
heat_subtypes.py		heat_subtypes.py
hi_lo.py		hi_lo.py
hi_lo_2.py		hi_lo_2.py
hi_lo_3.py		hi_lo_3.py
host_virus_barplot.py		host_virus_barplot.py
host_virus_elm_seq_heatmap.py		host_virus_elm_seq_heatmap.py
hprd_plot.py		hprd_plot.py
js_elmDist_host.py		js_elmDist_host.py
js_elmDist_host_flu.py		js_elmDist_host_flu.py
js_elmSeqDist_flu_flu.py		js_elmSeqDist_flu_flu.py
js_elmSeqDist_flus.py		js_elmSeqDist_flus.py
js_elmSeqDist_host_flu.py		js_elmSeqDist_host_flu.py
js_elmSeqDist_host_flu_2.py		js_elmSeqDist_host_flu_2.py
js_elmSeqDist_host_flu_2_dists.py		js_elmSeqDist_host_flu_2_dists.py
js_elmSeqDist_host_flu_fuzzyELMmatches.py		js_elmSeqDist_host_flu_fuzzyELMmatches.py
js_elmSeqDist_host_flu_fuzzyELMmatches_2.py		js_elmSeqDist_host_flu_fuzzyELMmatches_2.py
js_elmSeqDist_host_host_fuzzyELMmatches.py		js_elmSeqDist_host_host_fuzzyELMmatches.py
js_elmSeqDist_hosts.py		js_elmSeqDist_hosts.py
js_flu_elms.py		js_flu_elms.py
js_seqDist_hosts.py		js_seqDist_hosts.py
look_at_flu.py		look_at_flu.py
look_at_polPA_all.py		look_at_polPA_all.py
look_at_polPA_mapk.py		look_at_polPA_mapk.py
look_at_uniq_seqs.py		look_at_uniq_seqs.py
makeELMdict.py		makeELMdict.py
mammal_bird.py		mammal_bird.py
mammal_bird_same.py		mammal_bird_same.py
markov_chain.py		markov_chain.py
matchELMpattern.py		matchELMpattern.py
matchELMpattern_once.py		matchELMpattern_once.py
mkTestData.py		mkTestData.py
mk_aa_freq.py		mk_aa_freq.py
mk_aa_freq_all.py		mk_aa_freq_all.py
mk_chunks.py		mk_chunks.py
mk_freq.py		mk_freq.py
mk_random_seq.py		mk_random_seq.py
mk_simple_fasta.py		mk_simple_fasta.py
mk_simple_patterns.py		mk_simple_patterns.py
mk_single_member_clusters.py		mk_single_member_clusters.py

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A project that uses the ELM database to to determine the source organism of an influenza sequence.

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A project to find the source-organism of a flu sequence based on the specificity of functional sites.

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