aertslab/hydrop_data_analysis-v1.1.zip
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aertslab-hydrop_data_analysis-059bf5a
.gitignore
207 Bytes
HyDrop-ATAC
1_demult.ipynb
39.4 kB
2_vsn_pipeline.ipynb
17.9 kB
3_cistopic.ipynb
16.4 MB
4_qc_graphs.ipynb
407.9 kB
5_traces_script.ipynb
125.4 kB
6_dar_heatmap.ipynb
4.2 MB
cell_type_finetuned
lamp5.csv
13.5 kB
lef1.csv
8.4 kB
nxph3.csv
21.5 kB
pvalb.csv
27.3 kB
HyDrop-ATAC_barnyard
1_barnyard_pycistopic.ipynb
2.3 MB
2_generate_barnyard_from_fragments.ipynb
47.0 kB
fragments
HYA__7d0f30__20210305_barnyard_MCF-7_MMel_1-1_S1.sinto.fragments.tsv
170 Bytes
HYA__932b0e__20210309_mouse_cortex_MCF-7_PC3_1-1_S2.sinto.fragments.tsv
173 Bytes
HYA__af8d60__20210309_mouse_cortex_MCF-7_PC3_1-2_S3.sinto.fragments.tsv
173 Bytes
README.txt
112 Bytes
HyDrop-Barcode_qc
.ipynb_checkpoints
1_calculate_barcode_accuracy-checkpoint.ipynb
13.3 kB
2_analyse_barcode_accuracy-checkpoint.ipynb
3.5 kB
1_calculate_barcode_accuracy.ipynb
17.4 kB
2_analyse_barcode_accuracy.ipynb
8.0 kB
fastq
HYA__combined__20210323_cortex_phu_dv_etssb_1-1_S1_R2.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
164 Bytes
HYA__combined__20210323_cortex_phu_dv_etssb_1-2_S2_R2.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
164 Bytes
HYA__combined__20210323_cortex_phu_dv_etssb_1-3_S3_R2.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
164 Bytes
HYA__combined__20210323_cortex_phu_dv_etssb_1-4_S4_R2.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
164 Bytes
HYA__combined__20210323_cortex_phu_dv_etssb_1-5_S5_R2.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
164 Bytes
HYR__666332__20210412_mouse_cortex_sa_S1_R2_001.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
165 Bytes
HYR__c47998__20210412_mouse_cortex_sb_S2_R2_001.BCONLY.SUB.CORR.fastq.gz.corrected.bc_stats.tsv
165 Bytes
HyDrop-RNA
.ipynb_checkpoints
2_mapping-checkpoint.ipynb
11.9 kB
3_scanpy-checkpoint.ipynb
5.2 MB
1_demult.ipynb
6.0 kB
2_mapping.ipynb
11.9 kB
3_scanpy.ipynb
5.2 MB
4_extra_scanpy_fly.ipynb
1.4 MB
scanpy
hydrop-rna_mouse_cortex_finalann.loom
32.6 MB
lasso
Drd1.csv
3.4 kB
d2_msn.csv
2.9 kB
dbl.csv
1.3 kB
np-3.csv
4.7 kB
unknown.csv
822 Bytes
HyDrop-RNA_barnyard
1_count_matrix_barnyard.ipynb
140.7 kB
2_count_matrix_barnyard_internal_method_comparison.ipynb
54.0 kB
3_count_matrix_barnyard_old_designs.ipynb
22.6 kB
HyDrop-RNA_publicdata_comparison
.ipynb_checkpoints
1_initial_naive_comparison-checkpoint.ipynb
141.5 kB
2_download_indrop_dropseq_data-checkpoint.ipynb
18.5 kB
3a_dropseq_1_naive_mapping-checkpoint.ipynb
16.8 kB
3b_indrop_1_naive_mapping-checkpoint.ipynb
25.4 kB
4a_star_stats_qc-checkpoint.ipynb
368.4 kB
4b_indrop_2_count_indices-checkpoint.ipynb
9.3 kB
4c_indrop_3_generate_new_indrop_whitelist-checkpoint.ipynb
5.7 kB
5a_dropseq_2_downsample_fastq-checkpoint.ipynb
4.6 kB
5b_dropseq_3_remap_downsampled_fastq-checkpoint.ipynb
27.1 kB
5c_indrop_4_remap_individual_fastq_indexed_whitelist-checkpoint.ipynb
15.4 kB
5d_indrop_5_remap_merged_fastq_indexed_whitelist-checkpoint.ipynb
21.3 kB
6a_analysis_indrop_dropseq-checkpoint.ipynb
66.0 kB
7a_dropseq_remap_downsampled_fastq_with_whitelist-checkpoint.ipynb
14.4 kB
7b_dropseq_analysis_with_whitelist-checkpoint.ipynb
7.9 kB
7c_10x_analysis-checkpoint.ipynb
74.4 kB
8_final_stats_comparison-checkpoint.ipynb
958.8 kB
fig8_supp2-checkpoint.tsv
760 Bytes
10x
nuclei_2k_filtered_gene_bc_matrices
mm10
barcodes.tsv
44.7 kB
genes.tsv
740.4 kB
nuclei_2k_metrics_summary.csv
667 Bytes
nuclei_900_filtered_gene_bc_matrices
mm10
barcodes.tsv
18.1 kB
genes.tsv
740.4 kB
nuclei_900_metrics_summary.csv
666 Bytes
1_initial_naive_comparison.ipynb
142.6 kB
2_download_indrop_dropseq_data.ipynb
18.5 kB
3a_dropseq_1_naive_mapping.ipynb
16.9 kB
3b_indrop_1_naive_mapping.ipynb
25.4 kB
4a_star_stats_qc.ipynb
368.4 kB
4b_indrop_2_count_indices.ipynb
9.3 kB
4c_indrop_3_generate_new_indrop_whitelist.ipynb
2.5 kB
5a_dropseq_2_downsample_fastq.ipynb
4.6 kB
5b_dropseq_3_remap_downsampled_fastq.ipynb
27.3 kB
5c_indrop_4_remap_individual_fastq_indexed_whitelist.ipynb
15.4 kB
5d_indrop_5_remap_merged_fastq_indexed_whitelist.ipynb
21.3 kB
6a_analysis_indrop_dropseq.ipynb
66.0 kB
7a_dropseq_remap_downsampled_fastq_with_whitelist.ipynb
14.4 kB
7b_dropseq_analysis_with_whitelist.ipynb
41.6 kB
7c_10x_analysis.ipynb
74.4 kB
8_final_stats_comparison.ipynb
958.8 kB
SRR1853178_adata.tsv
875.7 kB
SRR1853179_adata.tsv
1.2 MB
SRR1853180_adata.tsv
784.0 kB
SRR1853181_adata.tsv
1.0 MB
SRR1853182_adata.tsv
1.0 MB
SRR1853183_adata.tsv
1.1 MB
SRR1853184_adata.tsv
541.2 kB
bc_count_raw
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390.8 kB
SRR10545069_3.bccount.tsv
419.8 kB
SRR10545070_3.bccount.tsv
412.4 kB
SRR10545071_3.bccount.tsv
407.7 kB
SRR10545072_3.bccount.tsv
380.1 kB
SRR10545073_3.bccount.tsv
404.7 kB
SRR10545074_3.bccount.tsv
386.6 kB
SRR10545075_3.bccount.tsv
424.5 kB
SRR10545076_3.bccount.tsv
404.8 kB
SRR10545077_3.bccount.tsv
409.9 kB
SRR10545078_3.bccount.tsv
410.5 kB
SRR10545079_3.bccount.tsv
425.0 kB
comparison_dataframe.tsv
5.6 MB
demultiplexed_dropseq
SRR1853178.Solo.out
Gene
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660 Bytes
Summary_numbers.csv
139 Bytes
GeneFull
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684 Bytes
filtered
barcodes.tsv
34.4 kB
features.tsv
1.3 MB
SRR1853179.Solo.out
Gene
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Summary_numbers.csv
140 Bytes
GeneFull
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filtered
barcodes.tsv
28.8 kB
features.tsv
1.3 MB
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barcodes.tsv
64.8 MB
features.tsv
1.3 MB
SRR1853180.Solo.out
Gene
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Summary_numbers.csv
140 Bytes
GeneFull
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filtered
barcodes.tsv
22.4 kB
features.tsv
1.3 MB
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barcodes.tsv
44.5 MB
features.tsv
1.3 MB
SRR1853181.Solo.out
Gene
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660 Bytes
Summary_numbers.csv
139 Bytes
GeneFull
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682 Bytes
filtered
barcodes.tsv
23.2 kB
features.tsv
1.3 MB
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barcodes.tsv
44.6 MB
features.tsv
1.3 MB
SRR1853182.Solo.out
Gene
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Summary_numbers.csv
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GeneFull
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features.tsv
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barcodes.tsv
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features.tsv
1.3 MB
SRR1853183.Solo.out
Gene
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Summary_numbers.csv
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GeneFull
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filtered
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features.tsv
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barcodes.tsv
37.5 MB
features.tsv
1.3 MB
SRR1853184.Solo.out
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Summary_numbers.csv
140 Bytes
GeneFull
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filtered
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25.5 kB
features.tsv
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barcodes.tsv
95.7 MB
features.tsv
1.3 MB
demultiplexed_dropseq_sub
SRR1853178.Solo.out
Gene
Summary.csv
660 Bytes
GeneFull
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685 Bytes
filtered
barcodes.tsv
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features.tsv
1.3 MB
SRR1853179.Solo.out
Gene
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GeneFull
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filtered
barcodes.tsv
28.3 kB
features.tsv
1.3 MB
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barcodes.tsv
62.1 MB
features.tsv
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SRR1853180.Solo.out
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GeneFull
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filtered
barcodes.tsv
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features.tsv
1.3 MB
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barcodes.tsv
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features.tsv
1.3 MB
SRR1853181.Solo.out
Gene
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GeneFull
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barcodes.tsv
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features.tsv
1.3 MB
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barcodes.tsv
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features.tsv
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SRR1853182.Solo.out
Gene
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GeneFull
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683 Bytes
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barcodes.tsv
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features.tsv
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barcodes.tsv
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features.tsv
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SRR1853183.Solo.out
Gene
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GeneFull
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barcodes.tsv
29.3 kB
features.tsv
1.3 MB
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barcodes.tsv
37.4 MB
features.tsv
1.3 MB
SRR1853184.Solo.out
Gene
Summary.csv
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GeneFull
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683 Bytes
filtered
barcodes.tsv
23.1 kB
features.tsv
1.3 MB
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barcodes.tsv
67.8 MB
features.tsv
1.3 MB
demultiplexed_dropseq_sub_whitelist
SRR1853178.Solo.out
Gene
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671 Bytes
filtered
barcodes.tsv
36.9 kB
features.tsv
1.3 MB
filtered_6600
barcodes.tsv
63.3 kB
features.tsv
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barcodes.tsv
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features.tsv
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barcodes.tsv
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features.tsv
1.3 MB
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barcodes.tsv
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features.tsv
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SRR1853179.Solo.out
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features.tsv
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72.8 kB
features.tsv
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features.tsv
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GeneFull
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31.2 kB
features.tsv
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barcodes.tsv
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features.tsv
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SRR1853180.Solo.out
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features.tsv
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barcodes.tsv
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features.tsv
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features.tsv
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features.tsv
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features.tsv
1.3 MB
SRR1853181.Solo.out
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features.tsv
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barcodes.tsv
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features.tsv
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features.tsv
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features.tsv
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SRR1853182.Solo.out
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features.tsv
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features.tsv
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SRR1853183.Solo.out
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features.tsv
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SRR1853184.Solo.out
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features.tsv
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features.tsv
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features.tsv
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SRR10545068.Solo.out
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Summary_numbers.csv
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SRR10545069.Solo.out
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features.tsv
1.3 MB
SRR10545072.Solo.out
Gene
Summary.csv
668 Bytes
Summary_numbers.csv
147 Bytes
filtered
barcodes.tsv
374.2 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
692 Bytes
filtered
barcodes.tsv
372.8 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545073.Solo.out
Gene
Summary.csv
667 Bytes
Summary_numbers.csv
146 Bytes
filtered
barcodes.tsv
378.8 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
690 Bytes
filtered
barcodes.tsv
376.9 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545074.Solo.out
Gene
Summary.csv
669 Bytes
Summary_numbers.csv
148 Bytes
filtered
barcodes.tsv
374.8 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
693 Bytes
filtered
barcodes.tsv
373.7 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545075.Solo.out
Gene
Summary.csv
669 Bytes
Summary_numbers.csv
148 Bytes
filtered
barcodes.tsv
347.3 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
692 Bytes
filtered
barcodes.tsv
345.8 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545076.Solo.out
Gene
Summary.csv
667 Bytes
Summary_numbers.csv
146 Bytes
filtered
barcodes.tsv
341.9 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
693 Bytes
filtered
barcodes.tsv
341.8 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545077.Solo.out
Gene
Summary.csv
666 Bytes
Summary_numbers.csv
145 Bytes
filtered
barcodes.tsv
339.8 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
690 Bytes
filtered
barcodes.tsv
337.7 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545078.Solo.out
Gene
Summary.csv
668 Bytes
filtered
barcodes.tsv
339.6 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
691 Bytes
filtered
barcodes.tsv
338.2 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
SRR10545079.Solo.out
Gene
Summary.csv
662 Bytes
filtered
barcodes.tsv
335.3 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
GeneFull
Summary.csv
688 Bytes
filtered
barcodes.tsv
334.6 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
merged.Solo.out
Gene
Summary.csv
676 Bytes
Summary_numbers.csv
155 Bytes
filtered
barcodes.tsv
371.1 kB
features.tsv
1.3 MB
filtered_27094
barcodes.tsv
549.2 kB
features.tsv
1.3 MB
filtered_31293
barcodes.tsv
562.8 kB
features.tsv
1.3 MB
GeneFull
Summary.csv
700 Bytes
filtered
barcodes.tsv
369.9 kB
features.tsv
1.3 MB
raw
barcodes.tsv
39.8 MB
features.tsv
1.3 MB
indropmerged_adata.tsv
3.9 MB
plts_pub
compar_public.svg
57.9 kB
compar_public_soft.png
286.1 kB
compar_public_soft.svg
59.0 kB
plts_python
.ipynb_checkpoints
indrop_starsoloqc-checkpoint.png
213.5 kB
all_starsoloqc.png
1.5 MB
all_starsoloqc.svg
132.7 kB
dropseq_starsoloqc.png
351.4 kB
dropseq_starsoloqc_sub_whitelist.png
216.5 kB
indrop_starsoloqc.png
316.6 kB
tables
10x_nuclei_2k_filtered_gene_bc_matrices.tsv
375.7 kB
10x_nuclei_900_filtered_gene_bc_matrices.tsv
160.2 kB
GSE140883_P10_1.ngenes.tsv
171.3 kB
GSE140883_P10_1.numis.tsv
171.9 kB
GSE140883_P10_2.ngenes.tsv
133.8 kB
GSE140883_P10_2.numis.tsv
134.2 kB
GSE140883_P15NR_1.ngenes.tsv
89.3 kB
GSE140883_P15NR_1.numis.tsv
89.8 kB
GSE140883_P15NR_2.ngenes.tsv
136.3 kB
GSE140883_P15NR_2.numis.tsv
136.6 kB
GSE140883_P15TR_1.ngenes.tsv
180.4 kB
GSE140883_P15TR_1.numis.tsv
181.0 kB
GSE140883_P15TR_2.ngenes.tsv
95.1 kB
GSE140883_P15TR_2.numis.tsv
95.8 kB
GSE140883_P20NR_1.ngenes.tsv
83.8 kB
GSE140883_P20NR_1.numis.tsv
84.6 kB
GSE140883_P20NR_2.ngenes.tsv
89.1 kB
GSE140883_P20NR_2.numis.tsv
90.9 kB
GSE140883_P20TR_1.ngenes.tsv
171.6 kB
GSE140883_P20TR_1.numis.tsv
172.1 kB
GSE140883_P20TR_2.ngenes.tsv
114.2 kB
GSE140883_P20TR_2.numis.tsv
114.7 kB
comparison_dataframe.tsv
5.6 MB
df_ngenes_cat.csv
1.5 MB
df_ngenes_cat_dropseq.csv
948.0 kB
df_ngenes_cat_indrop.csv
1.5 MB
df_numis_cat.csv
1.5 MB
df_numis_cat_dropseq.csv
955.4 kB
df_numis_cat_indrop.csv
1.5 MB
dropseq_SRR1853178_adata.tsv
875.7 kB
dropseq_SRR1853179_adata.tsv
1.2 MB
dropseq_SRR1853180_adata.tsv
784.0 kB
dropseq_SRR1853181_adata.tsv
1.0 MB
dropseq_SRR1853182_adata.tsv
1.0 MB
dropseq_SRR1853183_adata.tsv
1.1 MB
dropseq_SRR1853184_adata.tsv
541.2 kB
dropseq_whitelisted_SRR1853178_adata.tsv
888.1 kB
dropseq_whitelisted_SRR1853179_adata.tsv
1.2 MB
dropseq_whitelisted_SRR1853180_adata.tsv
792.7 kB
dropseq_whitelisted_SRR1853181_adata.tsv
1.0 MB
dropseq_whitelisted_SRR1853182_adata.tsv
1.0 MB
dropseq_whitelisted_SRR1853183_adata.tsv
1.1 MB
dropseq_whitelisted_SRR1853184_adata.tsv
542.1 kB
hydrop_adata.tsv
1.6 MB
indrop_merged_adata.tsv
3.9 MB
README.md
1.1 kB
manuscript_beadqc
atacqc
atacqc_acryd_Snap-11.tiff
2.1 MB
atacqc_atac_Snap-13.tiff
1.8 MB
bhb_intensity.py
9.5 kB
dtt
BIS-0mins_Snap-134.tiff
2.3 MB
BIS-15mins_Snap-146.tiff
2.2 MB
BIS-50mins_Snap-151.tiff
2.3 MB
intensities.xlsx
27.5 kB
isoampseries
iso_postbc_AcryD2-cropped.png
565.6 kB
iso_postbc_AcryD2-cropped.svg
855.7 kB
iso_postbc_AcryD2.tif
657.3 kB
iso_postbc_polyA2-cropped.png
385.7 kB
iso_postbc_polyA2-cropped.svg
594.5 kB
iso_postbc_polyA2.tif
443.2 kB
iso_prebc_AcryD2-cropped.png
537.9 kB
iso_prebc_AcryD2-cropped.svg
827.4 kB
iso_prebc_AcryD2.tif
635.2 kB
rnaqc
rnaqc_acrydpost_Snap-37.tiff
2.3 MB
rnaqc_acrydpre_Snap-35.tiff
2.1 MB
rnaqc_pa_Snap-43.tiff
2.1 MB
subbccounts
BC1
Snap-216.tiff
1.0 MB
Snap-216_mask.tif
10.0 MB
Snap-217.tiff
2.1 MB
Snap-218.tiff
984.6 kB
Snap-218_mask.tif
10.7 MB
Snap-219.tiff
2.0 MB
Snap-220.tiff
1.0 MB
Snap-220_mask.tif
10.2 MB
Snap-221.tiff
2.0 MB
BC2
Snap-226.tiff
1.1 MB
Snap-226_mask.tif
9.9 MB
Snap-227.tiff
2.0 MB
Snap-228.tiff
1.1 MB
Snap-228_mask.tif
10.5 MB
Snap-229.tiff
2.0 MB
Snap-230.tiff
1.2 MB
Snap-230_mask.tif
10.3 MB
Snap-231.tiff
2.1 MB
BC3
Snap-236.tiff
1.1 MB
Snap-236_mask.tif
9.6 MB
Snap-237.tiff
2.0 MB
Snap-241.tiff
1.1 MB
Snap-241_mask.tif
10.1 MB
Snap-242.tiff
2.0 MB
Snap-243.tiff
1.2 MB
Snap-243_mask.tif
11.5 MB
Snap-244.tiff
2.3 MB
manuscript_data_tables
fig_2a_dataframe.tsv.gz
17.5 kB
fig_2d_e_f_dataframe.tsv.gz
53.3 MB
fig_3a_dataframe.tsv.gz
246.2 kB
fig_3b_dataframe.tsv.gz
29.7 kB
fig_3c_comparison_dataframe.tsv.gz
1.4 MB
fig_3i_dataframe.tsv.gz
45.3 kB
resources
20200227_bc1.txt
1.1 kB
20200227_bc2.txt
1.1 kB
20200227_bc3.txt
1.1 kB
beep_silent.wav
63.2 kB