data_and_scripts.zip
HumanCRC
data
Gut2020.RData
252.8 kB
Human_crc_clin.csv
7.2 kB
PT_relatedness.RData
35.7 kB
fig4_related.RData
680.9 MB
mutations
B001P.txt
101.2 kB
B001T.txt
56.9 kB
B002P.txt
71.0 kB
B002T.txt
95.2 kB
B003P.txt
68.9 kB
B003T.txt
75.4 kB
B004P.txt
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B004T.txt
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B005P.txt
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B005T.txt
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B006P.txt
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B006T.txt
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B007T.txt
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B008P.txt
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B008T.txt
72.1 kB
B009P.txt
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B009T.txt
106.5 kB
B010P.txt
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B010T.txt
1.0 MB
B012P.txt
79.1 kB
B012T.txt
144.0 kB
B013P.txt
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B013T.txt
1.5 MB
B014P.txt
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B014T.txt
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B015P.txt
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B015T.txt
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B016P.txt
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B016T.txt
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B017T.txt
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B018P.txt
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B018T.txt
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B019P.txt
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B019T.txt
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B020P.txt
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B020T.txt
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B021P.txt
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B021T.txt
81.5 kB
B022P.txt
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B022T.txt
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B023P.txt
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B023T.txt
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B024P.txt
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B024T.txt
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B025T.txt
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B026P.txt
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B030T.txt
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B031P.txt
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B031T.txt
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B033P.txt
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B033T.txt
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B034P.txt
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B035T.txt
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B036P.txt
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B036T.txt
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B037T.txt
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B038P.txt
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B039T.txt
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B041T.txt
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B042T.txt
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B044P.txt
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B044T.txt
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B046P.txt
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B046T.txt
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B048P.txt
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B048T.txt
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B049P.txt
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B049T.txt
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B050P.txt
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B050T.txt
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B051P.txt
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B052T.txt
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B053P.txt
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B053T.txt
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B079T.txt
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B099T.txt
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B100P.txt
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B100T.txt
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B102P.txt
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B102T.txt
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B104P.txt
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B104T.txt
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B105P.txt
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B105T.txt
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B106P.txt
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B106T.txt
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B108P.txt
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B108T.txt
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B110P.txt
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B110T.txt
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B111P.txt
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B111T.txt
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B112P.txt
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B112T.txt
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B113P.txt
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B113T.txt
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B114P.txt
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B114T.txt
65.3 kB
B116P.txt
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B116T.txt
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B118P.txt
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B118T.txt
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B119P.txt
123.2 kB
B119T.txt
77.1 kB
B120P.txt
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B120T.txt
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B122P.txt
61.2 kB
B122T.txt
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B123P.txt
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B123T.txt
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B124P.txt
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B124T.txt
51.0 kB
B125P.txt
107.9 kB
B125T.txt
159.6 kB
B126P.txt
1.1 MB
B126T.txt
77.7 kB
readme.txt
777 Bytes
scripts
0Paper1_Fig4_human_crc.ipynb
938.5 kB
CNVPlottingFunctions.R
5.6 kB
PacBio
data
.ipynb_checkpoints
readme-checkpoint.txt
0 Bytes
trees
Apc68_P1.nwk
79.4 kB
Apc68_P2.nwk
106.1 kB
Apc68_P3.nwk
67.9 kB
Apc68_P4.nwk
123.1 kB
Apc68_P5-1.nwk
76.0 kB
Apc68_P5-2.nwk
41.7 kB
Apc68_P5-3.nwk
41.8 kB
Apc68_P5-4.nwk
53.9 kB
Apc68_P5-5.nwk
86.0 kB
Apc68_P5.nwk
169.3 kB
Apc71_P3.nwk
163.8 kB
Apc72_P1.nwk
243.0 kB
Apc72_P2.nwk
151.9 kB
Apc72_P4.nwk
264.8 kB
Apc72_P5.nwk
226.3 kB
Apc72_P6.nwk
230.4 kB
Apc72_P8.nwk
186.7 kB
Apc72_P9.nwk
227.4 kB
Apc75_P11.nwk
74.7 kB
Apc75_P3.nwk
57.0 kB
Apc75_P5.nwk
80.0 kB
Apc75_P8.nwk
110.8 kB
IBD132_T1.nwk
176.7 kB
IBD142_T1.nwk
385.1 kB
IBD142_T2.nwk
392.1 kB
IBD142_T5.nwk
173.7 kB
IBD148_T1.nwk
242.0 kB
IBD148_T3.nwk
272.1 kB
IBD151_T4.nwk
30.5 kB
IBD16_T.nwk
308.3 kB
IBD17_T4.nwk
26.6 kB
IBD18_T3.nwk
106.9 kB
IBD18_T4.nwk
70.5 kB
IBD19_T1.nwk
86.3 kB
IBD19_T3.nwk
128.6 kB
IBD19_T4.nwk
115.4 kB
IBD19_T5.nwk
91.3 kB
IBD2_T2.nwk
10.3 kB
IBD2_T3.nwk
11.0 kB
IBD47_T1.nwk
136.5 kB
IBD47_T4.nwk
16.3 kB
IBD47_T5.nwk
49.6 kB
IBD47_T6.nwk
51.3 kB
IBD47_T8.nwk
184.2 kB
IBD49_T1.nwk
40.8 kB
IBD49_T3.nwk
74.0 kB
IBD4_T.nwk
210.5 kB
IBD50_T.nwk
134.9 kB
IBD5_T.nwk
316.3 kB
IBD65_T1.nwk
15.8 kB
IBD65_T3.nwk
25.2 kB
IBD66_T.nwk
104.0 kB
WT1_N7.nwk
110.9 kB
WT2_N5.nwk
276.3 kB
readme.txt
1.0 kB
scripts
Reproductivity
.ipynb_checkpoints
0.0.Supplementary-mouse_weight-checkpoint.ipynb
72.3 kB
1.1.concatenate_oneNoneT-checkpoint.ipynb
6.3 kB
1.2.CRC10X2.R_remove_germline-checkpoint.ipynb
8.5 kB
1.3.filteringTree_frequency-checkpoint.ipynb
6.4 MB
1.3.filteringTree_frequency_plot-checkpoint.ipynb
209.5 kB
1.4.R_remove_same_sequences-checkpoint.ipynb
762.5 kB
1.5.CRC_vs_fly-checkpoint.ipynb
682.5 kB
2.1.R_mutation_stats_IBD&Immune-checkpoint.ipynb
464.3 kB
2.1.fig1_R_mutation_stats_CRC&Apc-checkpoint.ipynb
1.2 MB
2.2.fig2_SFS_CRC&Apc-checkpoint.ipynb
256.4 kB
2.3.plotTree_2panel&circular_CRC10X2_recolor-checkpoint.ipynb
136.4 kB
2.4.iqtree&rescale_tree-checkpoint.ipynb
11.3 kB
3.1.CRC10X_timing_downsampling-checkpoint.ipynb
12.0 kB
4.1.R_pairwise_genetic_distance_CRC-checkpoint.ipynb
507.2 kB
4.2.tree_resolution_crispr_smalt_calculate-checkpoint.ipynb
50.5 kB
4.2.tree_resolution_crispr_smalt_plot-checkpoint.ipynb
334.5 kB
5.1.plotTree_2panel&circular_recolor-checkpoint.ipynb
83.4 kB
s2.iqtree_filteredNT_re-checkpoint.sbatch
2.4 kB
0.0.Supplementary-mouse_weight.ipynb
72.3 kB
1.1.concatenate_oneNoneT.ipynb
6.3 kB
1.2.CRC10X2.R_remove_germline.ipynb
8.5 kB
1.3.filteringTree_frequency_plot.ipynb
209.5 kB
1.4.R_remove_same_sequences.ipynb
762.5 kB
1.5.CRC_vs_fly.ipynb
682.5 kB
2.1.fig1_R_mutation_stats_CRC&Apc.ipynb
1.2 MB
2.2.fig2_SFS_CRC&Apc.ipynb
256.4 kB
2.3.plotTree_2panel&circular_CRC10X2_recolor.ipynb
136.4 kB
2.4.iqtree&rescale_tree.ipynb
11.3 kB
3.1.CRC10X_timing_downsampling.ipynb
12.0 kB
4.1.R_pairwise_genetic_distance_CRC.ipynb
507.2 kB
4.2.tree_resolution_crispr_smalt_calculate.ipynb
50.5 kB
4.2.tree_resolution_crispr_smalt_plot.ipynb
334.5 kB
5.1.plotTree_2panel&circular_recolor.ipynb
83.4 kB
SMALT pipline
.ipynb_checkpoints
01-2.pbccs_minimap_CRC10X2-checkpoint.sbatch
3.0 kB
01.pbccs_minimap_CRC10X2-checkpoint.sbatch
3.0 kB
01.pbccs_minimap_IBD-checkpoint.sbatch
3.0 kB
02.parse_feature_YC-checkpoint.py
6.9 kB
02.run_parse_feature_YC-checkpoint.sbatch
1.1 kB
03.run_minimap-checkpoint.sbatch
2.1 kB
04-5-Copy1.run_usearch0.97-checkpoint.sbatch
2.0 kB
01.pbccs_minimap_IBD.sbatch
3.0 kB
02.parse_feature_YC.py
6.9 kB
02.run_parse_feature_YC.sbatch
1.1 kB
03.run_minimap.sbatch
2.1 kB
04.run_usearch0.99.sbatch
2.0 kB
05.generate_consensus.py
11.0 kB
05.run_generate_consensus0.99.sbatch
1.4 kB
WGS
data
mouse_wgs.maf
54.9 MB
readme.txt
823 Bytes
script
ABC
ABC_SMC_TumorSimul3D_SMALT_LineageTracing.py
29.8 kB
Apc_Np_timing_inference
68_node.R
4.2 kB
72_node.R
4.2 kB
IBD_Np_inference
get_Np.R
3.0 kB
prune.py
3.7 kB
scRNAseq
data
filteredCountsMatrix.rds
207.7 MB
metadata.rds
1.1 MB
rawCountsMatrix.rds
266.6 MB
readme.txt
1.3 kB
scripts
step00summaryQC.ipynb
30.0 kB
step01DataClean.ipynb
620.5 kB
step02Integrate.ipynb
6.4 MB
step03NpCor_GSVA.ipynb
3.1 MB
step04miloR.ipynb
2.4 MB
step05_1cellchatMain.ipynb
1.8 MB
step05_2cellchatIMM.ipynb
3.1 MB
step05_3cellchatEpi.ipynb
1.9 MB
step06multiNicheNet.ipynb
3.3 MB