Repository revision
13:d3fad161b318

Repository 'hicexplorer_hicfindtads'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads

hicFindTADs tool metadata
Miscellaneous
hicFindTADs
identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin
hicexplorer_hicfindtads
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/3.4.1.0
3.4.1.0
hicFindTADs --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/3.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/3.4.1.0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/3.3.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.4.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.8.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.8.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.7.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicfindtads/hicexplorer_hicfindtads/1.7.1.0
hicexplorer_hicfindtads
Requirements (dependencies defined in the <requirements> tag set)
name version type
hicexplorer 3.4.1 package
Functional tests
name inputs outputs required files
Test-1 minBoundaryDistance: 5000
precomputedZscore_conditional|step: 15000
precomputedZscore_conditional|precomputedZscore_selector: scratch
precomputedZscore_conditional|maxDepth: 30000
multiple_comparison_conditional|multiple_comparison_selector: fdr
multiple_comparison_conditional|threshold: 0.8
precomputedZscore_conditional|minDepth: 15000
matrix_h5_cooler: small_test_matrix.h5
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
attributes: name
small_test_matrix.h5
name
Test-2 precomputedZscore_conditional|scoreFile: find_TADs/multiFDR_tad_score.bm
minBoundaryDistance: 5000
precomputedZscore_conditional|precomputedZscore_selector: precomputed
multiple_comparison_conditional|multiple_comparison_selector: fdr
precomputedZscore_conditional|zscoreMatrix: find_TADs/multiFDR_zscore_matrix.h5
multiple_comparison_conditional|threshold: 0.1
matrix_h5_cooler: small_test_matrix.h5
attributes: name
attributes: name
attributes: name
attributes: name
small_test_matrix.h5
find_TADs/multiFDR_tad_score.bm
find_TADs/multiFDR_zscore_matrix.h5
name