bartongroup/two_pass_alignment_pipeline-v0.1.zip
bartongroup-two_pass_alignment_pipeline-225ac87
.gitignore
2.3 kB
.gitmodules
99 Bytes
2passpipeline.yml
115 Bytes
README.md
2.7 kB
annotations
arabidopsis
fetch_annotations.sh
765 Bytes
human
fetch_annotations.sh
730 Bytes
mouse
fetch_annotations.sh
715 Bytes
yeast
fetch_annotations.sh
818 Bytes
images
rulegraph.png
328.6 kB
rulegraph.svg
12.9 kB
rulegraph_sim.png
748.5 kB
rulegraph_sim.svg
21.4 kB
notebooks
benchmark_two_pass_alignment.ipynb
390.6 kB
benchmark_two_pass_transcript_assembly.ipynb
492.6 kB
decision_trees.ipynb
944.3 kB
figures
arabidopsis_decision_tree_1_confusion_matrix.svg
5.2 kB
arabidopsis_decision_tree_2_confusion_matrix.svg
5.2 kB
arabidopsis_drs_stringtie_benchmark.svg
24.2 kB
arabidopsis_isoseq_stringtie_benchmark.svg
21.0 kB
arabidopsis_lr_donor_score_confusion_matrix.svg
5.5 kB
arabidopsis_lr_scores_confusion_matrix.svg
16.1 kB
arath_junc_decision_tree_1_final.svg
46.0 kB
arath_junc_decision_tree_2_final.svg
64.3 kB
correct_percentage_filtered_2pass.svg
33.5 kB
correct_percentage_flair.svg
26.4 kB
correct_percentage_naive_2pass.svg
26.5 kB
feature_importances.svg
7.7 kB
human_cdna_stringtie_benchmark.svg
23.3 kB
human_decision_tree_1_confusion_matrix.svg
5.2 kB
human_decision_tree_2_confusion_matrix.svg
5.2 kB
human_drs_stringtie_benchmark.svg
25.7 kB
human_isoseq_stringtie_benchmark.svg
26.2 kB
incorrect_percentage_filtered_2pass.svg
55.9 kB
incorrect_percentage_flair.svg
44.1 kB
individual_metric_confusion_matrices.svg
19.2 kB
jad_annot_vs_unannot.svg
11.7 kB
mouse_cdna_stringtie_benchmark.svg
21.7 kB
mouse_drs_stringtie_benchmark.svg
22.2 kB
primary_donor_acceptor_metric_confusion_matrices.svg
10.0 kB
quantification_spearmanr_filtered_2pass.svg
32.1 kB
sequence_lr_model_diagram.svg
52.0 kB
simulated_data_identity.svg
18.5 kB
simulated_data_indels.svg
21.2 kB
simulated_data_mismatches.svg
21.6 kB
simulated_data_stringtie_benchmark.svg
23.9 kB
two_pass_method.svg
102.6 kB
yeast_drs_stringtie_benchmark.svg
26.0 kB
figures_final
figure1.png
290.7 kB
figure1.svg
3.7 MB
figure2.png
341.9 kB
figure2.svg
685.8 kB
figure3.png
594.2 kB
figure3.svg
307.6 kB
figure4.png
693.1 kB
figure4.svg
140.4 kB
figure5.png
417.5 kB
figure5.svg
155.1 kB
figure6.png
989.2 kB
figure6.svg
307.6 kB
suppfigure1.png
265.0 kB
suppfigure1.svg
202.0 kB
suppfigure2.png
327.2 kB
suppfigure2.svg
207.3 kB
suppfigure3.png
199.4 kB
suppfigure3.svg
38.9 kB
suppfigure4.png
181.7 kB
suppfigure4.svg
30.5 kB
suppfigure5.png
518.4 kB
suppfigure5.svg
673.6 kB
suppfigure6.png
858.4 kB
suppfigure6.svg
212.4 kB
flm_example_figures.ipynb
13.7 kB
read_simulation.ipynb
115.2 kB
pipeline
Snakefile
1.4 kB
arabidopsis_drs
config.yml
1.9 kB
fetch_data.sh
3.7 kB
arabidopsis_isoseq
config.yml
1.5 kB
human_cdna
config.yml
1.9 kB
human_drs
config.yml
1.9 kB
fetch_data.sh
1.9 kB
human_isoseq
config.yml
2.1 kB
mouse_cdna
config.yml
1.6 kB
mouse_drs
config.yml
1.6 kB
yeast_drs
config.yml
1.8 kB
rules
2passtools.snakefile
3.2 kB
assembly.snakefile
991 Bytes
benchmarking.snakefile
1.2 kB
env_yamls
2passtools.yml
252 Bytes
bedtools.yml
84 Bytes
flair.yml
124 Bytes
minimap2.yml
99 Bytes
stringtie.yml
106 Bytes
yanosim.yml
198 Bytes
flair.snakefile
838 Bytes
input.snakefile
2.6 kB
minimap2.snakefile
3.2 kB
simulation.snakefile
2.1 kB
scripts
get_sim_counts_from_reads.py
1.4 kB
minimap2
score_simulated.py
5.1 kB