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Some useful scripts for biological data analysis (ChIP-seq)

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241 Commits
compare_scripts
compare_scripts
 
 
pipeline
pipeline
 
 
.DS_Store
.DS_Store
 
 
.make_model.py.swp
.make_model.py.swp
 
 
COPYING
COPYING
 
 
README.md
README.md
 
 
bed_to_bedgraph_fasta.py
bed_to_bedgraph_fasta.py
 
 
bed_to_fasta.py
bed_to_fasta.py
 
 
bed_to_fasta_2.py
bed_to_fasta_2.py
 
 
bed_to_mcot_format.py
bed_to_mcot_format.py
 
 
bed_to_wig_fasta.py
bed_to_wig_fasta.py
 
 
binome_and_corr_tests.py
binome_and_corr_tests.py
 
 
binome_test.py
binome_test.py
 
 
bootstrap_for_bamm.jl
bootstrap_for_bamm.jl
 
 
bootstrap_for_bamm.py
bootstrap_for_bamm.py
 
 
bootstrap_for_inmode.jl
bootstrap_for_inmode.jl
 
 
bootstrap_for_inmode.py
bootstrap_for_inmode.py
 
 
bootstrap_for_pwm.jl
bootstrap_for_pwm.jl
 
 
bootstrap_for_pwm.py
bootstrap_for_pwm.py
 
 
calculate_number_of_sites_pwm.py
calculate_number_of_sites_pwm.py
 
 
calculate_roc_dipwm.py
calculate_roc_dipwm.py
 
 
calculate_roc_pwm.py
calculate_roc_pwm.py
 
 
calculate_threshold_for_bamm.jl
calculate_threshold_for_bamm.jl
 
 
calculate_threshold_for_inmode.jl
calculate_threshold_for_inmode.jl
 
 
calculate_threshold_for_pwm.jl
calculate_threshold_for_pwm.jl
 
 
clear_from_n.py
clear_from_n.py
 
 
compare_gene_ids.py
compare_gene_ids.py
 
 
compare_sites.py
compare_sites.py
 
 
compare_sites2.py
compare_sites2.py
 
 
compare_sites3-pypy.py
compare_sites3-pypy.py
 
 
compare_sites3.py
compare_sites3.py
 
 
compare_sites_old.py
compare_sites_old.py
 
 
complement_and_split_sites.py
complement_and_split_sites.py
 
 
corr_test.py
corr_test.py
 
 
extract_sites.py
extract_sites.py
 
 
get_genome_info.py
get_genome_info.py
 
 
get_pfm_from_bamm.py
get_pfm_from_bamm.py
 
 
get_promoters_ensembl_bed6.py
get_promoters_ensembl_bed6.py
 
 
get_promoters_ensemble_gtf.py
get_promoters_ensemble_gtf.py
 
 
get_random_peaks.py
get_random_peaks.py
 
 
get_random_samples_bed.py
get_random_samples_bed.py
 
 
get_threshold_by_fp_numpy.py
get_threshold_by_fp_numpy.py
 
 
get_threshold_for_bamm.py
get_threshold_for_bamm.py
 
 
get_threshold_for_inmode.py
get_threshold_for_inmode.py
 
 
get_threshold_for_pwm.py
get_threshold_for_pwm.py
 
 
get_top_peaks.py
get_top_peaks.py
 
 
gtf_to_bed.py
gtf_to_bed.py
 
 
homer_to_meme.py
homer_to_meme.py
 
 
homer_to_pwm.py
homer_to_pwm.py
 
 
make_ROC_Levitsky.py
make_ROC_Levitsky.py
 
 
make_ROC_My.py
make_ROC_My.py
 
 
make_background.py
make_background.py
 
 
make_model.py
make_model.py
 
 
make_oBAMM_pypy.py
make_oBAMM_pypy.py
 
 
make_oPWM.py
make_oPWM.py
 
 
make_oPWM_pypy.py
make_oPWM_pypy.py
 
 
montecarlo.py
montecarlo.py
 
 
montecarlo_scores.jl
montecarlo_scores.jl
 
 
parse_best_inmode_scan.py
parse_best_inmode_scan.py
 
 
parse_chipmunk_results.py
parse_chipmunk_results.py
 
 
parse_dichipmunk_results.py
parse_dichipmunk_results.py
 
 
parse_inmode_scan.py
parse_inmode_scan.py
 
 
parse_sitega_scan.py
parse_sitega_scan.py
 
 
pcm_to_pfm.py
pcm_to_pfm.py
 
 
peaks_intersection_with_bed.py
peaks_intersection_with_bed.py
 
 
peaks_intersection_with_bed6.py
peaks_intersection_with_bed6.py
 
 
peaks_intersection_with_fantom5_enchancer.py
peaks_intersection_with_fantom5_enchancer.py
 
 
peaks_intersection_with_fantom5_peaks.py
peaks_intersection_with_fantom5_peaks.py
 
 
peaks_intersection_with_promoters.py
peaks_intersection_with_promoters.py
 
 
pfm_to_pwm.py
pfm_to_pwm.py
 
 
pipeline.py
pipeline.py
 
 
pipeline3.1-nopypy.py
pipeline3.1-nopypy.py
 
 
pipeline3.1-only-denovo.py
pipeline3.1-only-denovo.py
 
 
pipeline3.1-smp3.py
pipeline3.1-smp3.py
 
 
pipeline3.1-threshold.py
pipeline3.1-threshold.py
 
 
pipeline3.1.py
pipeline3.1.py
 
 
pipeline3.py
pipeline3.py
 
 
pipeline_chipmunk_bamm.py
pipeline_chipmunk_bamm.py
 
 
pipeline_chipmunk_inmode.py
pipeline_chipmunk_inmode.py
 
 
pipeline_inmode.py
pipeline_inmode.py
 
 
pipeline_inmode_bamm.py
pipeline_inmode_bamm.py
 
 
plot_best_score.py
plot_best_score.py
 
 
prepare_fasta_for_chipmunk.py
prepare_fasta_for_chipmunk.py
 
 
prepare_peaks.py
prepare_peaks.py
 
 
reverse_complemet_matrix.py
reverse_complemet_matrix.py
 
 
scan_best_by_bamm.py
scan_best_by_bamm.py
 
 
scan_best_by_inmode.jl
scan_best_by_inmode.jl
 
 
scan_best_by_inmode.py
scan_best_by_inmode.py
 
 
scan_best_by_inmode_alt.py
scan_best_by_inmode_alt.py
 
 
scan_best_by_pwm.py
scan_best_by_pwm.py
 
 
scan_by_bamm.py
scan_by_bamm.py
 
 
scan_by_dipwm.py
scan_by_dipwm.py
 
 
scan_by_pwm.py
scan_by_pwm.py
 
 
scan_genome_by_bamm.py
scan_genome_by_bamm.py
 
 
score_to_pvalue.py
score_to_pvalue.py
 
 
touzet_bamm.py
touzet_bamm.py
 
 
touzet_bamm_np.py
touzet_bamm_np.py
 
 
touzet_pwm.py
touzet_pwm.py
 
 
touzet_pwm_np.py
touzet_pwm_np.py
 
 

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Some useful scripts for biological data analysis (ChIP-seq)

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Some useful scripts for biological data analysis (ChIP-seq)

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