Sung-Huan/ANNOgesic-v.1.0.1.zip
Sung-Huan-ANNOgesic-6365406
.gitignore
20 Bytes
CITATION.cff
477 Bytes
Dockerfile
7.5 kB
LICENSE
909 Bytes
MANIFEST.in
63 Bytes
Makefile
1.4 kB
README.rst
6.9 kB
Table_dependency_version.txt
1.9 kB
annogesiclib
TSS_upstream.py
6.3 kB
TSSpredator_parser.py
1.9 kB
args_container.py
61.8 kB
blast_class.py
1.4 kB
change_db_format.py
549 Bytes
check_orphan.py
14.2 kB
check_srna_overlap.py
3.2 kB
circRNA_detection.py
8.3 kB
circrna.py
26.1 kB
color_png.py
3.9 kB
combine_frag_tex.py
3.8 kB
combine_gff.py
5.0 kB
compare_sRNA_sORF.py
3.3 kB
compare_srna_promoter.py
3.3 kB
compare_srna_term.py
4.0 kB
compare_tran_term.py
7.7 kB
controller.py
54.5 kB
converter.py
23.2 kB
coverage_detection.py
8.1 kB
crispr.py
13.8 kB
detect_coverage_term.py
24.5 kB
detect_operon.py
14.7 kB
detect_utr.py
34.3 kB
expression.py
3.9 kB
extract_RBS.py
8.6 kB
extract_psortb.py
6.1 kB
extract_sRNA_info.py
12.9 kB
extract_sec_info.py
1.2 kB
fill_gap.py
8.5 kB
filter_TSS_pro.py
1.4 kB
filter_low_expression.py
5.1 kB
format_fixer.py
4.5 kB
gen_TSS_type.py
15.8 kB
gen_promoter_table.py
2.3 kB
gen_screenshots.py
5.6 kB
gen_srna_output.py
17.3 kB
gen_svg.py
3.2 kB
gen_table_tran.py
7.1 kB
gene_express_analysis.py
11.6 kB
gene_ontology.py
13.0 kB
get_Rfam_ribo.py
993 Bytes
get_input.py
3.7 kB
get_inter_seq.py
12.8 kB
get_polyT.py
17.7 kB
get_srna_poly_u.py
6.0 kB
get_target_fasta.py
4.5 kB
gff3.py
3.4 kB
goterm.py
7.8 kB
helper.py
15.3 kB
lib_reader.py
3.0 kB
map_ribos.py
1.6 kB
meme.py
21.2 kB
merge_feature.py
10.0 kB
merge_manual.py
27.7 kB
merge_rnaplex_rnaup.py
31.7 kB
merge_sRNA.py
24.7 kB
modify_rbs_table.py
2.0 kB
multiparser.py
17.0 kB
operon.py
4.4 kB
optimize.py
4.0 kB
optimize_TSSpredator.py
44.3 kB
output_cutoff_table.py
2.3 kB
overlap.py
3.3 kB
parser_wig.py
2.1 kB
paths.py
25.3 kB
plot_PPI.py
10.6 kB
plot_TSS_venn.py
6.3 kB
plot_coverage_table.py
1.9 kB
plot_mountain.py
1.9 kB
plot_tran.py
1.4 kB
potential_target.py
6.4 kB
ppi.py
26.0 kB
print_rank_all.py
984 Bytes
projectcreator.py
1.0 kB
ratt.py
12.7 kB
rbs_overlap.py
2.7 kB
recompute_RBS.py
8.4 kB
reorganize_table.py
2.8 kB
ribo_gff.py
7.0 kB
ribos.py
16.1 kB
sORF_detection.py
46.5 kB
sORF_intergenic.py
5.6 kB
sRNA_antisense.py
3.4 kB
sRNA_class.py
14.2 kB
sRNA_filter_frag.py
2.1 kB
sRNA_filter_min_utr.py
1.1 kB
sRNA_intergenic.py
33.7 kB
sRNA_utr_derived.py
37.2 kB
screen.py
3.5 kB
seq_editer.py
4.1 kB
seqmodifier.py
1.6 kB
snp.py
16.9 kB
sorf.py
9.7 kB
splice_parser.py
852 Bytes
srna.py
55.1 kB
srna_target.py
24.9 kB
stat_TA_comparison.py
18.0 kB
stat_TSSpredator.py
4.9 kB
stat_operon.py
3.8 kB
stat_sorf.py
9.0 kB
stat_sublocal.py
4.6 kB
stat_term.py
11.0 kB
sublocal.py
13.1 kB
terminator.py
30.4 kB
transcript.py
18.0 kB
transcript_SNP.py
18.0 kB
transcript_detection.py
8.8 kB
tsspredator.py
27.3 kB
utr.py
4.3 kB
validate_gene.py
5.2 kB
bin
annogesic
113.0 kB
comparison
README.md
979 Bytes
compare_TSS_Mendoza_Vargas.py
1.6 kB
compare_TSS_Salgado.py
2.1 kB
compare_operon_door.py
2.6 kB
compare_operon_regulondb.py
2.3 kB
compare_promoter_regulondb.py
1.7 kB
compare_sORF.py
1.7 kB
compare_srna.py
2.4 kB
compare_term_ecocyc.py
1.6 kB
compare_term_regulon.py
2.0 kB
compare_tran.py
1.9 kB
compare_utr.py
4.1 kB
gff3.py
3.3 kB
database
Rfam_RNA_thermometer_ID.csv
576 Bytes
Rfam_riboswitch_ID.csv
1.5 kB
sRNA_database_BSRD.fa
234.6 kB
docs
Makefile
7.4 kB
make.bat
7.3 kB
source
conf.py
9.3 kB
docker.rst
2.8 kB
index.rst
5.7 kB
installation.rst
2.9 kB
license.rst
864 Bytes
logo
READemption_logo.png
5.4 kB
annogesic_logo_white.png
2.3 kB
logo_annogesic.pdf
3.9 kB
logo_annogesic.png
1.5 kB
questions.rst
6.3 kB
required.rst
5.2 kB
subcommands.rst
198.5 kB
tutorial.rst
74.1 kB
user_manual.md
9.5 kB
get_package_database.sh
11.4 kB
run_test.py
122 Bytes
setup.py
1.0 kB
tests
mock_args_container.py
70 Bytes
mock_gff3.py
1.6 kB
mock_helper.py
1.3 kB
test_TSSpredator.py
1.7 kB
test_blast_class.py
2.6 kB
test_change_db_format.py
1.1 kB
test_check_orphan.py
12.0 kB
test_circRNA.py
10.0 kB
test_circrna.py
12.5 kB
test_color_png.py
2.4 kB
test_combine_frag_tex.py
5.1 kB
test_combine_gff.py
10.1 kB
test_compare_sRNA_sORF.py
3.9 kB
test_converter.py
28.6 kB
test_coverage_detection.py
6.5 kB
test_detect_coverage_term.py
14.1 kB
test_detect_operon.py
10.9 kB
test_detect_utr.py
16.1 kB
test_expresssion.py
2.8 kB
test_extract_RBS.py
5.5 kB
test_extract_psortb.py
9.4 kB
test_extract_sRNA_info.py
11.6 kB
test_fill_gap.py
6.0 kB
test_filter_TSS_pro.py
2.6 kB
test_filter_low_expression.py
4.7 kB
test_format_fixer.py
6.0 kB
test_gen_screenshots.py
5.0 kB
test_gen_srna_output.py
8.1 kB
test_gen_svg.py
2.9 kB
test_gen_table_tran.py
2.4 kB
test_gene_express_analysis.py
7.3 kB
test_gene_ontology.py
15.1 kB
test_get_Rfam_ribo.py
3.9 kB
test_get_input.py
5.1 kB
test_get_inter_seq.py
6.0 kB
test_get_polyT.py
6.3 kB
test_get_target_fasta.py
4.9 kB
test_gff3.py
2.3 kB
test_goterm.py
2.6 kB
test_helper.py
5.5 kB
test_lib_reader.py
6.6 kB
test_meme.py
3.4 kB
test_merge_manual.py
18.6 kB
test_merge_rnaplex_rnaup.py
13.2 kB
test_merge_sRNA.py
13.5 kB
test_modify_rbs_table.py
1.8 kB
test_multiparser.py
10.2 kB
test_operon.py
3.6 kB
test_optimize.py
3.3 kB
test_optimize_TSSpredator.py
26.0 kB
test_parser_wig.py
1.8 kB
test_paths.py
3.6 kB
test_plot_PPI.py
7.5 kB
test_plot_TSS_venn.py
3.7 kB
test_plot_coverage_table.py
1.1 kB
test_plot_mountain.py
1.5 kB
test_potential_target.py
6.1 kB
test_ppi.py
13.1 kB
test_projectcreator.py
1.1 kB
test_ratt.py
14.7 kB
test_recompute_RBS.py
9.4 kB
test_ribo_gff.py
8.0 kB
test_ribos.py
20.6 kB
test_sORF_detection.py
21.9 kB
test_sORF_intergenic.py
3.9 kB
test_sRNA_class.py
8.1 kB
test_sRNA_intergenic.py
22.3 kB
test_sRNA_utr_derived.py
31.3 kB
test_screen.py
6.1 kB
test_seq_editer.py
2.4 kB
test_seqmodifier.py
1.3 kB
test_snp.py
10.2 kB
test_sorf.py
6.2 kB
test_splice_parser.py
1.4 kB
test_srna.py
18.8 kB
test_srna_target.py
8.9 kB
test_stat_TA_comparison.py
12.8 kB
test_stat_TSSpredater.py
3.0 kB
test_stat_operon.py
4.5 kB
test_stat_sorf.py
10.4 kB
test_stat_sublocal.py
3.5 kB
test_stat_term.py
6.7 kB
test_sublocal.py
4.9 kB
test_terminator.py
13.9 kB
test_transcript.py
11.3 kB
test_transcript_SNP.py
21.0 kB
test_transcript_detection.py
7.1 kB
test_tsspredator.py
18.9 kB
test_utr.py
5.7 kB
test_validate_gene.py
5.0 kB
uni_report.py
1.8 kB
tutorial_data
NC_009839_manual_TSS.gff
9.1 kB
mutation.csv
142 Bytes
replace_seq_id.py
1.1 kB
run.sh
18.6 kB
run_with_sigularity.sh
19.8 kB