scTensor Experiments: Data Preparation and Reproduction

public 1yr ago 0 bookmarks

View Workflow

Help improve this workflow!

This workflow has been published but could be further improved with some additional meta data:

Keyword(s) in categories input, output, operation

You can help improve this workflow by suggesting the addition or removal of keywords, suggest changes and report issues, or request to become a maintainer of the Workflow .

scTensor-experiments

About data preparation

Synthetic datasets: synthetic_datasets/data/README.md
Real datasets: real_datasets/data/README.md

Requirements

Bash: GNU bash, version 4.2.46(1)-release (x86_64-redhat-linux-gnu)
Snakemake: 5.3.0
Singularity: 3.5.3

How to reproduce this workflow

snakemake -j 4 --use-singularity # Local Machine
snakemake -j 32 --cluster qsub --latency-wait 600 --use-singularity # Open Grid Engine
snakemake -j 32 --cluster sbatch --latency-wait 600 --use-singularity # Slurm

License

Authors

Koki Tsuyuzaki
Manabu Ishii
Itoshi Nikaido

Code Snippets

shell:
    'src/preprocess_{wildcards.sample}.sh {output} > {log}'

SnakeMake From line 62 of real_datasets/Snakefile

shell:
    'src/groundtruth.sh {output} > {log}'

SnakeMake From line 76 of real_datasets/Snakefile

shell:
    'src/plot_groundtruth.sh {wildcards.sample} {output} > {log}'

SnakeMake From line 90 of real_datasets/Snakefile

shell:
    'src/labelpermutation.sh {input} {output.out1} {output.out2} > {log}'

SnakeMake From line 107 of real_datasets/Snakefile

shell:
    'src/labelpermutation2.sh {input} {output.out1} {output.out2} > {log}'

SnakeMake From line 124 of real_datasets/Snakefile

shell:
    'src/halpern.sh {input} {output.out1} {output.out2} > {log}'

SnakeMake From line 141 of real_datasets/Snakefile

shell:
    'src/cabelloaguilar.sh {input} {output.out1} {output.out2} > {log}'

SnakeMake From line 158 of real_datasets/Snakefile

shell:
    'src/previous_sctensor.sh {input} {output} > {log}'

SnakeMake From line 175 of real_datasets/Snakefile

shell:
    'src/sctensor.sh {input} {output} > {log}'

SnakeMake From line 192 of real_datasets/Snakefile

shell:
    'src/aggregate_previous_sctensor.sh {input} {output} > {log}'

SnakeMake From line 220 of real_datasets/Snakefile

shell:
    'src/aggregate_sctensor.sh {input} {output} > {log}'

SnakeMake From line 236 of real_datasets/Snakefile

shell:
    'src/roc_auc_bin_f.sh {input} {output} > {log}'

SnakeMake From line 266 of real_datasets/Snakefile

shell:
    'src/plot_roc_auc_f.sh {input} {output} > {log}'

SnakeMake From line 285 of real_datasets/Snakefile

shell:
    'src/plot_prc_aucpr_mcc.sh {input} {output} > {log}'

SnakeMake From line 305 of real_datasets/Snakefile

shell:
    'src/plot_auc.sh {output} > {log}'

SnakeMake From line 320 of real_datasets/Snakefile

shell:
    'src/plot_aucpr.sh {output} > {log}'

SnakeMake From line 335 of real_datasets/Snakefile

shell:
    'src/plot_f.sh {output} > {log}'

SnakeMake From line 350 of real_datasets/Snakefile

shell:
    'src/plot_mcc.sh {output} > {log}'

SnakeMake From line 365 of real_datasets/Snakefile

shell:
    'src/plot_fpr.sh {output} > {log}'

SnakeMake From line 380 of real_datasets/Snakefile

shell:
    'src/plot_fnr.sh {output} > {log}'

SnakeMake From line 395 of real_datasets/Snakefile

shell:
    'src/plot_pr.sh {output} > {log}'

SnakeMake From line 410 of real_datasets/Snakefile

shell:
    'src/plot_tr.sh {output} > {log}'

SnakeMake From line 425 of real_datasets/Snakefile

shell:
    'src/plot_time.sh {output} > {log}'

SnakeMake From line 440 of real_datasets/Snakefile

shell:
    'src/plot_memory.sh {output} > {log}'

SnakeMake From line 455 of real_datasets/Snakefile

shell:
    'src/plot_LR.sh {wildcards.binmethod} {wildcards.sample} {output} > {log}'

SnakeMake From line 478 of real_datasets/Snakefile

shell:
    'src/report.sh {input} {output} > {log}'

SnakeMake From line 493 of real_datasets/Snakefile

SLURM_RESTART_COUNT=2

echo $@

Rscript src/aggregate.R $@

Shell From line 11 of src/aggregate_previous_sctensor.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/aggregate.R $@

Shell From line 11 of src/aggregate_sctensor.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/cabelloaguilar.R $@

Shell From line 11 of src/cabelloaguilar.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/groundtruth.R $@

Shell From line 11 of src/groundtruth.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/halpern.R $@

Shell From line 11 of src/halpern.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/labelpermutation2.R $@

Shell From line 11 of src/labelpermutation2.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/labelpermutation.R $@

Shell From line 11 of src/labelpermutation.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_aucpr.R $@

Shell From line 11 of src/plot_aucpr.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_auc.R

Shell From line 11 of src/plot_auc.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fnr.R

Shell From line 11 of src/plot_fnr.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fpr.R

Shell From line 11 of src/plot_fpr.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_f.R

Shell From line 11 of src/plot_f.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_groundtruth.R $@

Shell From line 11 of src/plot_groundtruth.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_LR.R $@

Shell From line 11 of src/plot_LR.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_mcc.R

Shell From line 11 of src/plot_mcc.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_memory.R

Shell From line 11 of src/plot_memory.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_prc_aucpr_mcc.R $@

Shell From line 11 of src/plot_prc_aucpr_mcc.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_pr.R

Shell From line 11 of src/plot_pr.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_roc_auc_f.R $@

Shell From line 11 of src/plot_roc_auc_f.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_time.R

Shell From line 11 of src/plot_time.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_tr.R

Shell From line 11 of src/plot_tr.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/previous_sctensor.R $@

Shell From line 11 of src/previous_sctensor.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/report.R $@

Shell From line 11 of src/report.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/roc_auc_bin_f.R $@

Shell From line 11 of src/roc_auc_bin_f.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/sctensor.R $@

Shell From line 11 of src/sctensor.sh

shell:
    'src/cellcellsimulate.sh {wildcards.e} {output} > {log}'

SnakeMake From line 114 of synthetic_datasets/Snakefile

shell:
    'src/groundtruth.sh {output} > {log}'

SnakeMake From line 126 of synthetic_datasets/Snakefile

shell:
    'src/plot_groundtruth.sh {wildcards.sample} {output} > {log}'

SnakeMake From line 140 of synthetic_datasets/Snakefile

shell:
    'src/{wildcards.othermethod}.sh {input} {output} > {log}'

SnakeMake From line 161 of synthetic_datasets/Snakefile

shell:
    'src/previous_sctensor.sh {input} {output} > {log}'

SnakeMake From line 179 of synthetic_datasets/Snakefile

shell:
    'src/sctensor.sh {input} {output} > {log}'

SnakeMake From line 197 of synthetic_datasets/Snakefile

shell:
    'src/aggregate_previous_sctensor.sh {input} {output} > {log}'

SnakeMake From line 250 of synthetic_datasets/Snakefile

shell:
    'src/aggregate_previous_sctensor.sh {input} {output} > {log}'

SnakeMake From line 264 of synthetic_datasets/Snakefile

shell:
    'src/aggregate_previous_sctensor.sh {input} {output} > {log}'

SnakeMake From line 278 of synthetic_datasets/Snakefile

shell:
    'src/aggregate_sctensor.sh {input} {output} > {log}'

SnakeMake From line 292 of synthetic_datasets/Snakefile

shell:
    'src/aggregate_sctensor.sh {input} {output} > {log}'

SnakeMake From line 306 of synthetic_datasets/Snakefile

shell:
    'src/aggregate_sctensor.sh {input} {output} > {log}'

SnakeMake From line 320 of synthetic_datasets/Snakefile

shell:
    'src/roc_auc_bin_f.sh {input} {output} > {log}'

SnakeMake From line 354 of synthetic_datasets/Snakefile

shell:
    'src/plot_roc_auc_f.sh {input.in1} {input.in2} {input.in3} {output} > {log}'

SnakeMake From line 377 of synthetic_datasets/Snakefile

shell:
    'src/plot_prc_aucpr_mcc.sh {input.in1} {input.in2} {input.in3} {input.in4} {output} > {log}'

SnakeMake From line 398 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc.sh {wildcards.method} E2 {output} > {log}'

SnakeMake From line 468 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc_eachcci.sh {wildcards.method} E2 {output} > {log}'

SnakeMake From line 484 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc_merge.sh E2 {output} > {log}'

SnakeMake From line 499 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc.sh {wildcards.method} E5 {output} > {log}'

SnakeMake From line 515 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc_eachcci.sh {wildcards.method} E5 {output} > {log}'

SnakeMake From line 531 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc_merge.sh E5 {output} > {log}'

SnakeMake From line 546 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc.sh {wildcards.method} E10 {output} > {log}'

SnakeMake From line 562 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc_eachcci.sh {wildcards.method} E10 {output} > {log}'

SnakeMake From line 578 of synthetic_datasets/Snakefile

shell:
    'src/plot_auc_merge.sh E10 {output} > {log}'

SnakeMake From line 593 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr.sh {wildcards.method} E2 {output} > {log}'

SnakeMake From line 612 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr_eachcci.sh {wildcards.method} E2 {output} > {log}'

SnakeMake From line 628 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr_merge.sh E2 {output} > {log}'

SnakeMake From line 643 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr.sh {wildcards.method} E5 {output} > {log}'

SnakeMake From line 659 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr_eachcci.sh {wildcards.method} E5 {output} > {log}'

SnakeMake From line 675 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr_merge.sh E5 {output} > {log}'

SnakeMake From line 690 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr.sh {wildcards.method} E10 {output} > {log}'

SnakeMake From line 706 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr_eachcci.sh {wildcards.method} E10 {output} > {log}'

SnakeMake From line 722 of synthetic_datasets/Snakefile

shell:
    'src/plot_aucpr_merge.sh E10 {output} > {log}'

SnakeMake From line 737 of synthetic_datasets/Snakefile

shell:
    'src/plot_f.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 754 of synthetic_datasets/Snakefile

shell:
    'src/plot_f_eachcci.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 768 of synthetic_datasets/Snakefile

shell:
    'src/plot_f_merge.sh E2 {output} > {log}'

SnakeMake From line 783 of synthetic_datasets/Snakefile

shell:
    'src/plot_f.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 797 of synthetic_datasets/Snakefile

shell:
    'src/plot_f_eachcci.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 811 of synthetic_datasets/Snakefile

shell:
    'src/plot_f_merge.sh E5 {output} > {log}'

SnakeMake From line 826 of synthetic_datasets/Snakefile

shell:
    'src/plot_f.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 840 of synthetic_datasets/Snakefile

shell:
    'src/plot_f_eachcci.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 854 of synthetic_datasets/Snakefile

shell:
    'src/plot_f_merge.sh E10 {output} > {log}'

SnakeMake From line 869 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 886 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc_eachcci.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 900 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc_merge.sh E2 {output} > {log}'

SnakeMake From line 915 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 929 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc_eachcci.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 943 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc_merge.sh E5 {output} > {log}'

SnakeMake From line 958 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 972 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc_eachcci.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 986 of synthetic_datasets/Snakefile

shell:
    'src/plot_mcc_merge.sh E10 {output} > {log}'

SnakeMake From line 1001 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1018 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr_eachcci.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1032 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr_merge.sh E2 {output} > {log}'

SnakeMake From line 1047 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1061 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr_eachcci.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1075 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr_merge.sh E5 {output} > {log}'

SnakeMake From line 1090 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1104 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr_eachcci.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1118 of synthetic_datasets/Snakefile

shell:
    'src/plot_fpr_merge.sh E10 {output} > {log}'

SnakeMake From line 1133 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1150 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr_eachcci.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1164 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr_merge.sh E2 {output} > {log}'

SnakeMake From line 1179 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1193 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr_eachcci.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1207 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr_merge.sh E5 {output} > {log}'

SnakeMake From line 1222 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1236 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr_eachcci.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1250 of synthetic_datasets/Snakefile

shell:
    'src/plot_fnr_merge.sh E10 {output} > {log}'

SnakeMake From line 1265 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1282 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr_eachcci.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1296 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr_merge.sh E2 {output} > {log}'

SnakeMake From line 1311 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1325 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr_eachcci.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1339 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr_merge.sh E5 {output} > {log}'

SnakeMake From line 1354 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1368 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr_eachcci.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1382 of synthetic_datasets/Snakefile

shell:
    'src/plot_pr_merge.sh E10 {output} > {log}'

SnakeMake From line 1397 of synthetic_datasets/Snakefile

shell:
    'src/plot_tr.sh {output} > {log}'

SnakeMake From line 1415 of synthetic_datasets/Snakefile

shell:
    'src/plot_tr_eachcci.sh {output} > {log}'

SnakeMake From line 1430 of synthetic_datasets/Snakefile

shell:
    'src/plot_time.sh {wildcards.method} E2 {output} > {log}'

SnakeMake From line 1449 of synthetic_datasets/Snakefile

shell:
    'src/plot_time_merge.sh E2 {output} > {log}'

SnakeMake From line 1464 of synthetic_datasets/Snakefile

shell:
    'src/plot_time.sh {wildcards.method} E5 {output} > {log}'

SnakeMake From line 1480 of synthetic_datasets/Snakefile

shell:
    'src/plot_time_merge.sh E5 {output} > {log}'

SnakeMake From line 1495 of synthetic_datasets/Snakefile

shell:
    'src/plot_time.sh {wildcards.method} E10 {output} > {log}'

SnakeMake From line 1511 of synthetic_datasets/Snakefile

shell:
    'src/plot_time_merge.sh E10 {output} > {log}'

SnakeMake From line 1526 of synthetic_datasets/Snakefile

shell:
    'src/plot_memory.sh {wildcards.method} E2 {output} > {log}'

SnakeMake From line 1545 of synthetic_datasets/Snakefile

shell:
    'src/plot_memory_merge.sh E2 {output} > {log}'

SnakeMake From line 1560 of synthetic_datasets/Snakefile

shell:
    'src/plot_memory.sh {wildcards.method} E5 {output} > {log}'

SnakeMake From line 1576 of synthetic_datasets/Snakefile

shell:
    'src/plot_memory_merge.sh E5 {output} > {log}'

SnakeMake From line 1591 of synthetic_datasets/Snakefile

shell:
    'src/plot_memory.sh {wildcards.method} E10 {output} > {log}'

SnakeMake From line 1607 of synthetic_datasets/Snakefile

shell:
    'src/plot_memory_merge.sh E10 {output} > {log}'

SnakeMake From line 1622 of synthetic_datasets/Snakefile

shell:
    'src/plot_LR.sh {wildcards.binmethod} E2 {output} > {log}'

SnakeMake From line 1643 of synthetic_datasets/Snakefile

shell:
    'src/plot_LR.sh {wildcards.binmethod} E5 {output} > {log}'

SnakeMake From line 1661 of synthetic_datasets/Snakefile

shell:
    'src/plot_LR.sh {wildcards.binmethod} E10 {output} > {log}'

SnakeMake From line 1679 of synthetic_datasets/Snakefile

SLURM_RESTART_COUNT=2

echo $@

Rscript src/aggregate.R $@

Shell From line 11 of src/aggregate_previous_sctensor.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/aggregate.R $@

Shell From line 11 of src/aggregate_sctensor.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/cellcellsimulate.R $@

Shell From line 11 of src/cellcellsimulate.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/groundtruth.R $@

Shell From line 11 of src/groundtruth.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_auc_eachcci.R $@

Shell From line 11 of src/plot_auc_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_auc_merge.R $@

Shell From line 11 of src/plot_auc_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_aucpr_eachcci.R $@

Shell From line 11 of src/plot_aucpr_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_aucpr_merge.R $@

Shell From line 11 of src/plot_aucpr_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_aucpr.R $@

Shell From line 11 of src/plot_aucpr.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_auc.R $@

Shell From line 11 of src/plot_auc.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_f_eachcci.R $@

Shell From line 11 of src/plot_f_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_f_merge.R $@

Shell From line 11 of src/plot_f_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fnr_eachcci.R $@

Shell From line 11 of src/plot_fnr_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fnr_merge.R $@

Shell From line 11 of src/plot_fnr_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fnr.R $@

Shell From line 11 of src/plot_fnr.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fpr_eachcci.R $@

Shell From line 11 of src/plot_fpr_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fpr_merge.R $@

Shell From line 11 of src/plot_fpr_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_fpr.R $@

Shell From line 11 of src/plot_fpr.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_f.R $@

Shell From line 11 of src/plot_f.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_groundtruth.R $@

Shell From line 11 of src/plot_groundtruth.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_LR.R $@

Shell From line 11 of src/plot_LR.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_mcc_eachcci.R $@

Shell From line 11 of src/plot_mcc_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_mcc_merge.R $@

Shell From line 11 of src/plot_mcc_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_mcc.R $@

Shell From line 11 of src/plot_mcc.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_memory_merge.R $@

Shell From line 11 of src/plot_memory_merge.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_memory.R $@

Shell From line 11 of src/plot_memory.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_prc_aucpr_mcc.R $@

Shell From line 11 of src/plot_prc_aucpr_mcc.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_pr_eachcci.R $@

Shell From line 11 of src/plot_pr_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_pr_merge.R $@

Shell From line 11 of src/plot_pr_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_pr.R $@

Shell From line 11 of src/plot_pr.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/plot_roc_auc_f.R $@

Shell From line 11 of src/plot_roc_auc_f.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_time_merge.R $@

Shell From line 11 of src/plot_time_merge.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_time.R $@

Shell From line 11 of src/plot_time.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_tr_eachcci.R $@

Shell From line 11 of src/plot_tr_eachcci.sh

SLURM_RESTART_COUNT=2

Rscript src/plot_tr.R $@

Shell From line 11 of src/plot_tr.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/previous_sctensor.R $@

Shell From line 11 of src/previous_sctensor.sh

SLURM_RESTART_COUNT=2

Rscript src/roc_auc_bin_f.R $@

Shell From line 11 of src/roc_auc_bin_f.sh

SLURM_RESTART_COUNT=2

echo $@

Rscript src/sctensor.R $@

Shell From line 11 of src/sctensor.sh

ShowHide 184 more snippets with no or duplicated tags.

Comments

Support

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/rikenbit/scTensor-experiments

Name: sctensor-experiments

Version: 1

Badge:

Insert copied code into your website to add a link to this workflow.

License: None

Keywords:

scTensor Snakemake Data acquisition

Future updates

Related Workflows

psychip_snakemake — Show Details View Workflow

ENCODE pipeline for histone marks developed for the psychENCODE project

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...

raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake

Free

Near-real time tracking of SARS-CoV-2 in Connecticut

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...

JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode

Free

cellranger-snakemake-gke — Show Details View Workflow

snakemake workflow to run cellranger on a given bucket using gke.

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...

macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake

Free

ATLAS - Three commands to start analyzing your metagenome data

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...

raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics

Free

175

rna-seq-star-deseq2 — Show Details View Workflow

RNA-seq workflow using STAR and DESeq2

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...

Free

dna-seq-gatk-variant-calling — Show Details View Workflow

This Snakemake pipeline implements the GATK best-practices workflow

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...

VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA

Free