Mercurial > repos > bgruening > diffbind

comparison test-data/out_analysis_info.txt @ 11:4c7ab9995f9e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit cc4c1c4131518b9cbf986a1f252767ff73ca938e
author iuc
date Sat, 07 Apr 2018 15:45:41 -0400
parents
children
comparison
equal deleted inserted replaced
10:d7725c5596ab 11:4c7ab9995f9e
1 dba.count Info
2
3 4 Samples, 1394 sites in matrix (2141 total):
4 ID Tissue Condition Caller Intervals
5 1 MCF7_ER_1_bed MCF7_ER_1_bed Responsive macs 1556
6 2 MCF7_ER_2_bed MCF7_ER_2_bed Responsive macs 1046
7 3 BT474_ER_1_bed BT474_ER_1_bed Resistant macs 1080
8 4 BT474_ER_2_bed BT474_ER_2_bed Resistant macs 1122
9
10 dba.analyze Info
11
12 4 Samples, 1394 sites in matrix:
13 ID Tissue Condition Caller Intervals FRiP
14 1 MCF7_ER_1_bed MCF7_ER_1_bed Responsive counts 1394 0.38
15 2 MCF7_ER_2_bed MCF7_ER_2_bed Responsive counts 1394 0.22
16 3 BT474_ER_1_bed BT474_ER_1_bed Resistant counts 1394 0.27
17 4 BT474_ER_2_bed BT474_ER_2_bed Resistant counts 1394 0.25
18
19 1 Contrast:
20 Group1 Members1 Group2 Members2 DB.DESeq2
21 1 Responsive 2 Resistant 2 5
22
23 SessionInfo
24
25 R version 3.4.1 (2017-06-30)
26 Platform: x86_64-apple-darwin14.5.0 (64-bit)
27 Running under: OS X El Capitan 10.11.6
28
29 Matrix products: default
30 BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
31 LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
32
33 locale:
34 [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_US.UTF-8
35
36 attached base packages:
37 [1] parallel stats4 methods stats graphics grDevices utils
38 [8] datasets base
39
40 other attached packages:
41 [1] bindrcpp_0.2 rjson_0.2.15
42 [3] DiffBind_2.6.6 SummarizedExperiment_1.8.0
43 [5] DelayedArray_0.4.1 matrixStats_0.52.2
44 [7] Biobase_2.38.0 GenomicRanges_1.30.3
45 [9] GenomeInfoDb_1.14.0 IRanges_2.12.0
46 [11] S4Vectors_0.16.0 BiocGenerics_0.24.0
47 [13] getopt_1.20.0
48
49 loaded via a namespace (and not attached):
50 [1] Category_2.44.0 bitops_1.0-6 bit64_0.9-5
51 [4] RColorBrewer_1.1-2 progress_1.1.2 httr_1.3.1
52 [7] Rgraphviz_2.22.0 tools_3.4.1 backports_1.0.5
53 [10] R6_2.2.2 rpart_4.1-13 KernSmooth_2.23-15
54 [13] Hmisc_4.0-3 DBI_0.8 lazyeval_0.2.1
55 [16] colorspace_1.3-2 nnet_7.3-12 gridExtra_2.3
56 [19] DESeq2_1.18.1 prettyunits_1.0.2 bit_1.1-12
57 [22] compiler_3.4.1 sendmailR_1.2-1 graph_1.56.0
58 [25] htmlTable_1.9 labeling_0.3 rtracklayer_1.38.0
59 [28] caTools_1.17.1 scales_0.5.0 checkmate_1.8.2
60 [31] BatchJobs_1.6 genefilter_1.60.0 RBGL_1.54.0
61 [34] stringr_1.3.0 digest_0.6.12 Rsamtools_1.30.0
62 [37] foreign_0.8-67 AnnotationForge_1.20.0 XVector_0.18.0
63 [40] htmltools_0.3.6 base64enc_0.1-3 pkgconfig_2.0.1
64 [43] limma_3.34.6 htmlwidgets_1.0 rlang_0.2.0
65 [46] RSQLite_2.0 BBmisc_1.11 bindr_0.1.1
66 [49] GOstats_2.44.0 hwriter_1.3.2 BiocParallel_1.12.0
67 [52] gtools_3.5.0 acepack_1.4.1 dplyr_0.7.4
68 [55] RCurl_1.95-4.8 magrittr_1.5 Formula_1.2-1
69 [58] GO.db_3.5.0 GenomeInfoDbData_0.99.1 Matrix_1.2-12
70 [61] Rcpp_0.12.15 munsell_0.4.3 stringi_1.1.6
71 [64] edgeR_3.20.7 zlibbioc_1.24.0 gplots_3.0.1
72 [67] fail_1.3 plyr_1.8.4 grid_3.4.1
73 [70] blob_1.1.1 ggrepel_0.7.0 gdata_2.18.0
74 [73] lattice_0.20-34 Biostrings_2.46.0 splines_3.4.1
75 [76] GenomicFeatures_1.28.5 annotate_1.56.0 locfit_1.5-9.1
76 [79] knitr_1.20 pillar_1.2.1 systemPipeR_1.12.0
77 [82] geneplotter_1.56.0 biomaRt_2.34.2 glue_1.2.0
78 [85] XML_3.98-1.6 ShortRead_1.36.0 latticeExtra_0.6-28
79 [88] data.table_1.10.4 gtable_0.2.0 amap_0.8-14
80 [91] assertthat_0.2.0 ggplot2_2.2.1 xtable_1.8-2
81 [94] survival_2.40-1 tibble_1.4.2 pheatmap_1.0.8
82 [97] GenomicAlignments_1.14.1 AnnotationDbi_1.40.0 memoise_1.1.0
83 [100] cluster_2.0.6 brew_1.0-6 GSEABase_1.40.0