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gozdekibar · Feb 25, 2022 · 05693f6 · 05693f6
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Showing 24 changed files with 146 additions and 693 deletions.
diff --git a/PLAAC/.DS_Store b/PLAAC/.DS_Store
diff --git a/PLAAC/._.DS_Store b/PLAAC/._.DS_Store
diff --git a/PLAAC/._HG38_pep_PLAAC_clean.csv b/PLAAC/._HG38_pep_PLAAC_clean.csv
diff --git a/PLAAC/._HG38_pep_PLDs.txt b/PLAAC/._HG38_pep_PLDs.txt
diff --git a/PLAAC/._PLD99 b/PLAAC/._PLD99
diff --git a/PLAAC/._PLD_Plaac_table.xlsx b/PLAAC/._PLD_Plaac_table.xlsx
diff --git a/PLAAC/._plaac-master b/PLAAC/._plaac-master
diff --git a/PLAAC/._~$PLD_Plaac_table.xlsx b/PLAAC/._~$PLD_Plaac_table.xlsx
diff --git a/PLAAC/PLD99/._HG38_PDL_aromaticFrac.csv b/PLAAC/PLD99/._HG38_PDL_aromaticFrac.csv
diff --git a/PLAAC/PLD99/._HG38_pep_unique.fasta b/PLAAC/PLD99/._HG38_pep_unique.fasta
diff --git a/PLAAC/PLD99/._PLD.fasta b/PLAAC/PLD99/._PLD.fasta
diff --git a/PLAAC/PLD99/._PLD_99p.xlsx b/PLAAC/PLD99/._PLD_99p.xlsx
diff --git a/PLAAC/PLD99/._PLD_Plaac_table.xlsx b/PLAAC/PLD99/._PLD_Plaac_table.xlsx
diff --git a/PLAAC/PLD99/._PLD_seqs.csv b/PLAAC/PLD99/._PLD_seqs.csv
diff --git a/PLAAC/PLD99/._list.txt b/PLAAC/PLD99/._list.txt
diff --git a/PLAAC/PLD99/.ipynb_checkpoints/Untitled-checkpoint.ipynb b/PLAAC/PLD99/.ipynb_checkpoints/Untitled-checkpoint.ipynb
diff --git a/RNAbindingProteins/._41580_2018_BFnrm2017130_MOESM121_ESM.xlsx b/RNAbindingProteins/._41580_2018_BFnrm2017130_MOESM121_ESM.xlsx
diff --git a/RNAbindingProteins/._nrm.2017.130.pdf b/RNAbindingProteins/._nrm.2017.130.pdf
diff --git a/TFs/._AnnotationCoF.csv b/TFs/._AnnotationCoF.csv
diff --git a/TFs/._AnnotationTFs.csv b/TFs/._AnnotationTFs.csv
diff --git a/TFs/._TF_CF_IDs.xlsx b/TFs/._TF_CF_IDs.xlsx
diff --git a/annotations/.DS_Store b/annotations/.DS_Store
diff --git a/codesForPlots/PlotDot.ipynb b/codesForPlots/PlotDot.ipynb
@@ -20,9 +20,153 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "\n",
+      "DOSE v3.18.0  For help: https://guangchuangyu.github.io/software/DOSE\n",
+      "\n",
+      "If you use DOSE in published research, please cite:\n",
+      "Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609\n",
+      "\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘dplyr’\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:stats’:\n",
+      "\n",
+      "    filter, lag\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:base’:\n",
+      "\n",
+      "    intersect, setdiff, setequal, union\n",
+      "\n",
+      "\n",
+      "clusterProfiler v4.0.0  For help: https://guangchuangyu.github.io/software/clusterProfiler\n",
+      "\n",
+      "If you use clusterProfiler in published research, please cite:\n",
+      "Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘clusterProfiler’\n",
+      "\n",
+      "\n",
+      "The following object is masked from ‘package:stats’:\n",
+      "\n",
+      "    filter\n",
+      "\n",
+      "\n",
+      "Loading required package: AnnotationDbi\n",
+      "\n",
+      "Loading required package: stats4\n",
+      "\n",
+      "Loading required package: BiocGenerics\n",
+      "\n",
+      "Loading required package: parallel\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘BiocGenerics’\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:parallel’:\n",
+      "\n",
+      "    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n",
+      "    clusterExport, clusterMap, parApply, parCapply, parLapply,\n",
+      "    parLapplyLB, parRapply, parSapply, parSapplyLB\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:dplyr’:\n",
+      "\n",
+      "    combine, intersect, setdiff, union\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:stats’:\n",
+      "\n",
+      "    IQR, mad, sd, var, xtabs\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:base’:\n",
+      "\n",
+      "    Filter, Find, Map, Position, Reduce, anyDuplicated, append,\n",
+      "    as.data.frame, basename, cbind, colnames, dirname, do.call,\n",
+      "    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,\n",
+      "    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,\n",
+      "    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,\n",
+      "    tapply, union, unique, unsplit, which.max, which.min\n",
+      "\n",
+      "\n",
+      "Loading required package: Biobase\n",
+      "\n",
+      "Welcome to Bioconductor\n",
+      "\n",
+      "    Vignettes contain introductory material; view with\n",
+      "    'browseVignettes()'. To cite Bioconductor, see\n",
+      "    'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n",
+      "\n",
+      "\n",
+      "Loading required package: IRanges\n",
+      "\n",
+      "Loading required package: S4Vectors\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘S4Vectors’\n",
+      "\n",
+      "\n",
+      "The following object is masked from ‘package:clusterProfiler’:\n",
+      "\n",
+      "    rename\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:dplyr’:\n",
+      "\n",
+      "    first, rename\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:base’:\n",
+      "\n",
+      "    I, expand.grid, unname\n",
+      "\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘IRanges’\n",
+      "\n",
+      "\n",
+      "The following object is masked from ‘package:clusterProfiler’:\n",
+      "\n",
+      "    slice\n",
+      "\n",
+      "\n",
+      "The following objects are masked from ‘package:dplyr’:\n",
+      "\n",
+      "    collapse, desc, slice\n",
+      "\n",
+      "\n",
+      "\n",
+      "Attaching package: ‘AnnotationDbi’\n",
+      "\n",
+      "\n",
+      "The following object is masked from ‘package:clusterProfiler’:\n",
+      "\n",
+      "    select\n",
+      "\n",
+      "\n",
+      "The following object is masked from ‘package:dplyr’:\n",
+      "\n",
+      "    select\n",
+      "\n",
+      "\n",
+      "\n",
+      "\n"
+     ]
+    }
+   ],
    "source": [
     "library(DOSE)\n",
     "library(ggplot2)\n",

diff --git a/gmt_files/.DS_Store b/gmt_files/.DS_Store