Sanitize notebook cell numbers, update HiSeqV2

The version (date) of the Xena Browser HiSeqV2 file updated, but doesn't show
any visible downstream changes.

Ran `bash execute.sh` which refreshed some cell numbers that had become dirty.

Uploaded full datasets to figshare. See the following version-specific URL:
https://doi.org/10.6084/m9.figshare.3487685.v3

2.TCGA-process.ipynb

@@ -352,7 +352,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 7,
    "metadata": {
     "collapsed": true
    },
@@ -374,7 +374,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false
    },
@@ -385,7 +385,7 @@
        "{\"3'UTR\", \"5'Flank\", \"5'UTR\", 'IGR', 'Intron', 'Silent'}"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -397,7 +397,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 9,
    "metadata": {
     "collapsed": false
    },
@@ -441,7 +441,7 @@
        "1  TCGA-02-0003-01  chr10  TACC2      1"
       ]
      },
-     "execution_count": 12,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -467,7 +467,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 10,
    "metadata": {
     "collapsed": false
    },
@@ -508,7 +508,7 @@
        "1          2  chr12    A2M"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 10,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -522,7 +522,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 11,
    "metadata": {
     "collapsed": false
    },
@@ -572,7 +572,7 @@
        "1  TCGA-17-Z015-01  chr1  TPM3      1       7170   TPM3"
       ]
      },
-     "execution_count": 14,
+     "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -587,7 +587,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 12,
    "metadata": {
     "collapsed": false
    },
@@ -598,7 +598,7 @@
        "(8507, 21940)"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -615,7 +615,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 13,
    "metadata": {
     "collapsed": false
    },
@@ -626,7 +626,7 @@
        "'0.67% sample-gene pairs are mutated'"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -638,7 +638,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 14,
    "metadata": {
     "collapsed": false
    },
@@ -694,7 +694,7 @@
        "4   CSMD3   989"
       ]
      },
-     "execution_count": 17,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -706,7 +706,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 15,
    "metadata": {
     "collapsed": false
    },
@@ -762,7 +762,7 @@
        "4  TCGA-B5-A0JY-01       6151"
       ]
      },
-     "execution_count": 18,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -783,7 +783,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 16,
    "metadata": {
     "collapsed": false
    },
@@ -796,7 +796,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 17,
    "metadata": {
     "collapsed": false
    },
@@ -807,7 +807,7 @@
        "set()"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -825,7 +825,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
+   "execution_count": 18,
    "metadata": {
     "collapsed": false
    },
@@ -836,7 +836,7 @@
        "(10459, 20530)"
       ]
      },
-     "execution_count": 21,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -860,7 +860,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 19,
    "metadata": {
     "collapsed": false
    },
@@ -943,7 +943,7 @@
        "TCGA-02-2486-01  6.7716  15.3224  6.3377  2.2199  16.7832"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -964,7 +964,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 20,
    "metadata": {
     "collapsed": false
    },
@@ -975,7 +975,7 @@
        "7705"
       ]
      },
-     "execution_count": 23,
+     "execution_count": 20,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -987,7 +987,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 21,
    "metadata": {
     "collapsed": false
    },
@@ -1009,7 +1009,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 22,
    "metadata": {
     "collapsed": false
    },
@@ -1031,7 +1031,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 23,
    "metadata": {
     "collapsed": false
    },
@@ -1053,7 +1053,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 24,
    "metadata": {
     "collapsed": true
    },

download/HiSeqV2.json

@@ -14,7 +14,7 @@
  "label":"gene expression",
  "cohort":"TCGA Pan-Cancer (PANCAN)",
  "redistribution":true,
- "version":"2016-04-29",
+ "version":"2016-08-16",
  "tags":
  ["cancer", "non-small cell lung cancer", "gastric cancer",
   "pancancer", "Adrenal gland", "Esophagus", "Rectum", "Endometrium",