scripts

Bioinformatic scripts for various applications in Python and R. Please contact me for help / details.

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
PCA.py		PCA.py
README.md		README.md
acc2tax.py		acc2tax.py
acc2tax2.py		acc2tax2.py
adaptor_clip_fastq.py		adaptor_clip_fastq.py
add_filename_to_lines.py		add_filename_to_lines.py
bbPCRmap.py		bbPCRmap.py
bbPROBEmap.py		bbPROBEmap.py
bbmap_general.py		bbmap_general.py
bbmap_general_fast.py		bbmap_general_fast.py
bbmap_pacbio.py		bbmap_pacbio.py
binary_names.py		binary_names.py
blast-nest-filter.py		blast-nest-filter.py
blastfolder.py		blastfolder.py
blastfolderdb.py		blastfolderdb.py
bubble-tree.py		bubble-tree.py
burst.py		burst.py
calculate_diversity.R		calculate_diversity.R
cat_sra_parts.py		cat_sra_parts.py
centrifuge.py		centrifuge.py
centrifuge2taxtable.py		centrifuge2taxtable.py
check_origin.py		check_origin.py
chopfasta.py		chopfasta.py
common_names.py		common_names.py
convert_folder.py		convert_folder.py
corr_matrix1.R		corr_matrix1.R
count_samples.py		count_samples.py
fasta1line.py		fasta1line.py
fastp.py		fastp.py
fastq_add_sufffix.py		fastq_add_sufffix.py
fold2ps.py		fold2ps.py
fold2ps_noseq.py		fold2ps_noseq.py
gap-download.py		gap-download.py
gb2multifastaprot.py		gb2multifastaprot.py
gc.py		gc.py
gene-matrix-from-uclust4.py		gene-matrix-from-uclust4.py
genes2targets.py		genes2targets.py
get-numpts.py		get-numpts.py
get-region.py		get-region.py
get-seqs-from-file-not.py		get-seqs-from-file-not.py
get-seqs-from-file.py		get-seqs-from-file.py
get-seqs-from-uc.py		get-seqs-from-uc.py
get-seqs-largefile.py		get-seqs-largefile.py
get-seqs-para.py		get-seqs-para.py
get_first_contig.py		get_first_contig.py
gff2fasta.py		gff2fasta.py
heatmap.R		heatmap.R
join_hp_results_para.py		join_hp_results_para.py
kmerfreq.py		kmerfreq.py
kraken1.py		kraken1.py
kraken1_otutable.py		kraken1_otutable.py
kraken2.py		kraken2.py
kraken_top_mpa.py		kraken_top_mpa.py
lca4.py		lca4.py
lca_count.py		lca_count.py
list_compare.py		list_compare.py
macse.py		macse.py
mantel.py		mantel.py
mantelfolder.py		mantelfolder.py
maxbin.py		maxbin.py
meta_otu_table3.py		meta_otu_table3.py
metaphlan2folder.py		metaphlan2folder.py
metaphlan4folder.py		metaphlan4folder.py
miRNA_bbmap.py		miRNA_bbmap.py
minimap-noself.py		minimap-noself.py
n50folder.py		n50folder.py
ncbi_cds2gs.py		ncbi_cds2gs.py
numpt-borders.py		numpt-borders.py
numpt_overlap_sam.py		numpt_overlap_sam.py
order_scaffs.py		order_scaffs.py
otu_habitat.py		otu_habitat.py
para-count.py		para-count.py
pathtype.py		pathtype.py
pearson-q.py		pearson-q.py
pearson.py		pearson.py
primer_clip_fastq.py		primer_clip_fastq.py
rankseqs.py		rankseqs.py
rbo-dist.py		rbo-dist.py
read-histogram.py		read-histogram.py
reformat-para.py		reformat-para.py
revcomp		revcomp
revcomp2.py		revcomp2.py
sam4map.py		sam4map.py
seq2dict_func.py		seq2dict_func.py
shannons-filter.py		shannons-filter.py
simreads-para.py		simreads-para.py
sizesfolder.py		sizesfolder.py
soft2hardmask.py		soft2hardmask.py
species2taxid.py		species2taxid.py
sra_dl_fastq.py		sra_dl_fastq.py
table_from_uc.py		table_from_uc.py
tax2_16s.py		tax2_16s.py
tax_level.py		tax_level.py
tax_trace.pl		tax_trace.pl
trimmo.py		trimmo.py
ublast.py		ublast.py

theo-allnutt-bioinformatics/scripts

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