GitHub - rdgroussman/general: General repository for code of various functions

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General repository for code of various functions

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Name		Name	Last commit message	Last commit date
Latest commit History 53 Commits
treecolor		treecolor
DE_clusters.py		DE_clusters.py
Illumina_QC_AWS.sh		Illumina_QC_AWS.sh
SNP_ancestry.py		SNP_ancestry.py
check_hmmtab_for_dupes.py		check_hmmtab_for_dupes.py
clean_MMETSP.py		clean_MMETSP.py
combine_d1_contig_data.py		combine_d1_contig_data.py
combine_dmnd_uniq_taxids.py		combine_dmnd_uniq_taxids.py
combine_guppy_csv.py		combine_guppy_csv.py
count_custom_standards.py		count_custom_standards.py
count_delong_pplacer_csv_by_taxonomy.py		count_delong_pplacer_csv_by_taxonomy.py
count_kallisto_tpm_combined.py		count_kallisto_tpm_combined.py
count_lca_tab_by_taxonomy.py		count_lca_tab_by_taxonomy.py
count_m8_csv_by_taxonomy.py		count_m8_csv_by_taxonomy.py
count_pplacer_csv_by_edge.py		count_pplacer_csv_by_edge.py
count_pplacer_csv_by_taxonomy.py		count_pplacer_csv_by_taxonomy.py
count_standards.py		count_standards.py
custom_accession2taxid.py		custom_accession2taxid.py
d1.combine_contig_data_FPKMx.py		d1.combine_contig_data_FPKMx.py
d1.combine_contig_data_FPKMx_v2.py		d1.combine_contig_data_FPKMx_v2.py
d1.combine_count_sums.py		d1.combine_count_sums.py
d1.contig_data_by_contig_id.sh		d1.contig_data_by_contig_id.sh
d1.contig_data_by_pfam.sh		d1.contig_data_by_pfam.sh
d1.contig_data_by_pfam_FPKMx.sh		d1.contig_data_by_pfam_FPKMx.sh
d1.contig_data_by_pfam_local.sh		d1.contig_data_by_pfam_local.sh
d1.count_kofam_by_taxid_rawcounts.py		d1.count_kofam_by_taxid_rawcounts.py
d1.count_kofam_by_taxid_stdcounts.py		d1.count_kofam_by_taxid_stdcounts.py
d1.count_pfam_by_taxid_rawcounts.py		d1.count_pfam_by_taxid_rawcounts.py
d1.count_pfam_by_taxid_rawcounts2.py		d1.count_pfam_by_taxid_rawcounts2.py
d1.count_pfam_by_taxid_std_counts.py		d1.count_pfam_by_taxid_std_counts.py
d1.cumulative_contig_sums.py		d1.cumulative_contig_sums.py
d1.cumulative_count_sums.py		d1.cumulative_count_sums.py
d1.cumulative_pfam_sums.py		d1.cumulative_pfam_sums.py
d1.custom_contig_sums.py		d1.custom_contig_sums.py
d1.custom_contig_sums2.py		d1.custom_contig_sums2.py
d1.sum_by_group_and_kofam_FPKMx.py		d1.sum_by_group_and_kofam_FPKMx.py
d1.sum_by_group_and_kofam_FPKMx_4rain.py		d1.sum_by_group_and_kofam_FPKMx_4rain.py
d1.sum_by_group_and_pfam.py		d1.sum_by_group_and_pfam.py
d1.sum_by_group_and_pfam_FPKMx.py		d1.sum_by_group_and_pfam_FPKMx.py
d1.sum_by_group_and_pfam_FPKMx_all_data.py		d1.sum_by_group_and_pfam_FPKMx_all_data.py
d1.sum_by_group_and_pfam_FPKMx_all_data2.py		d1.sum_by_group_and_pfam_FPKMx_all_data2.py
d1.sum_by_group_and_pfam_FPKMx_all_data_4rain.py		d1.sum_by_group_and_pfam_FPKMx_all_data_4rain.py
d1.sum_by_group_and_pfam_FPKMx_all_data_4rain_4grp.py		d1.sum_by_group_and_pfam_FPKMx_all_data_4rain_4grp.py
d1.sum_by_group_and_pfam_FPKMx_all_data_4rain_custom_grp.py		d1.sum_by_group_and_pfam_FPKMx_all_data_4rain_custom_grp.py
d1.sum_by_group_and_pfam_FPKMx_v2.py		d1.sum_by_group_and_pfam_FPKMx_v2.py
d1.sum_by_group_and_pfam_stdnorm.py		d1.sum_by_group_and_pfam_stdnorm.py
d1.sum_by_nested_taxid.py		d1.sum_by_nested_taxid.py
d1.sum_by_nested_taxid_knums.py		d1.sum_by_nested_taxid_knums.py
d1.sum_raw_counts.py		d1.sum_raw_counts.py
dedupe_fasta_by_defline.py		dedupe_fasta_by_defline.py
diel1_pplacer.sh		diel1_pplacer.sh
diel_hmmer_sprouter.sh		diel_hmmer_sprouter.sh
extract_mmetsp-id_from_fasta.sh		extract_mmetsp-id_from_fasta.sh
extract_seqs_by_length.py		extract_seqs_by_length.py
extract_seqs_by_mmetsp_id.py		extract_seqs_by_mmetsp_id.py
filter_guppy_csv_by_pendant_length.py		filter_guppy_csv_by_pendant_length.py
filter_sto_by_hmmtab.py		filter_sto_by_hmmtab.py
filter_transrate_scores.py		filter_transrate_scores.py
fix_nr_multiaccession.py		fix_nr_multiaccession.py
fix_uclust_headers.py		fix_uclust_headers.py
fnames2.py		fnames2.py
fnames_to_kaiju_deflines.py		fnames_to_kaiju_deflines.py
force_unique_headers.py		force_unique_headers.py
get500bpupstream.py		get500bpupstream.py
get_taxonomy_from_taxid.py		get_taxonomy_from_taxid.py
gradients1_seed_sprouter.sh		gradients1_seed_sprouter.sh
graph_from_counts_output.py		graph_from_counts_output.py
hmmer_sprouter.sh		hmmer_sprouter.sh
hmmer_sprouter_pt2.sh		hmmer_sprouter_pt2.sh
hmmer_sprouter_ptI.sh		hmmer_sprouter_ptI.sh
kallisto_norm_factors.py		kallisto_norm_factors.py
kallisto_summary_filter.py		kallisto_summary_filter.py
keep_longest_frame.py		keep_longest_frame.py
link_CAMPEP_to_MMETSP_id.py		link_CAMPEP_to_MMETSP_id.py
listgrab.py		listgrab.py
listgrab_gzip.py		listgrab_gzip.py
listgrab_m8out_by_tax.py		listgrab_m8out_by_tax.py
listgrab_simple.py		listgrab_simple.py
listgrab_transrate.py		listgrab_transrate.py
logfattree.py		logfattree.py
look_no_hands.sh		look_no_hands.sh
mORFeus.py		mORFeus.py
make_seq_info_all.py		make_seq_info_all.py
memlog2graph.py		memlog2graph.py
mmetsp_clustering.sh		mmetsp_clustering.sh
normalize_by_RP.py		normalize_by_RP.py
order_taxa_fracts.py		order_taxa_fracts.py
parse_SINA_results.py		parse_SINA_results.py
parse_polgyenic_presence.py		parse_polgyenic_presence.py
parse_rapsearch.py		parse_rapsearch.py
parse_rapsearch_output.py		parse_rapsearch_output.py
plot_pplacer_counts_results.R		plot_pplacer_counts_results.R
rank_counts_from_diamond.py		rank_counts_from_diamond.py
rank_counts_from_pplacer.py		rank_counts_from_pplacer.py
record_mem_use.sh		record_mem_use.sh
reset_xml.py		reset_xml.py
seed_sprouter.sh		seed_sprouter.sh
sort_dmnd_lca_by_tax.py		sort_dmnd_lca_by_tax.py
taxify_dmnd_lca_taxids.py		taxify_dmnd_lca_taxids.py
taxify_taxa_fracts.py		taxify_taxa_fracts.py

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