upload data files

.gitignore

@@ -25,7 +25,7 @@
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-vignettes/data
+#vignettes/data
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth

vignettes/data/GSE60450_annotation.csv

@@ -0,0 +1,41 @@
+ENSEMBL,Type,Annotation
+ENSMUSG00000031805,SYMBOL,Jak3
+ENSMUSG00000031805,GENENAME,Janus kinase 3
+ENSMUSG00000033909,SYMBOL,Usp36
+ENSMUSG00000033909,GENENAME,ubiquitin specific peptidase 36
+ENSMUSG00000065524,SYMBOL,Mir135a-2
+ENSMUSG00000065524,GENENAME,microRNA 135a-2
+ENSMUSG00000030374,SYMBOL,Strn4
+ENSMUSG00000030374,GENENAME,"striatin, calmodulin binding protein 4"
+ENSMUSG00000098547,SYMBOL,Mir6921
+ENSMUSG00000098547,GENENAME,microRNA 6921
+ENSMUSG00000035629,SYMBOL,Rubcn
+ENSMUSG00000035629,GENENAME,"RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"
+ENSMUSG00000094053,SYMBOL,Scgb2b7
+ENSMUSG00000094053,GENENAME,"secretoglobin, family 2B, member 7"
+ENSMUSG00000055491,SYMBOL,Pprc1
+ENSMUSG00000055491,GENENAME,"peroxisome proliferative activated receptor, gamma, coactivator-related 1"
+ENSMUSG00000053080,SYMBOL,Zfta
+ENSMUSG00000053080,GENENAME,zinc finger translocation associated
+ENSMUSG00000039715,SYMBOL,Dync2i2
+ENSMUSG00000039715,GENENAME,dynein 2 intermediate chain 2
+ENSMUSG00000033475,SYMBOL,Tomm6
+ENSMUSG00000033475,GENENAME,translocase of outer mitochondrial membrane 6
+ENSMUSG00000026283,SYMBOL,Ing5
+ENSMUSG00000026283,GENENAME,"inhibitor of growth family, member 5"
+ENSMUSG00000037331,SYMBOL,Larp1
+ENSMUSG00000037331,GENENAME,"La ribonucleoprotein 1, translational regulator"
+ENSMUSG00000074489,SYMBOL,Bglap3
+ENSMUSG00000074489,GENENAME,bone gamma-carboxyglutamate protein 3
+ENSMUSG00000038246,SYMBOL,Fam50b
+ENSMUSG00000038246,GENENAME,"family with sequence similarity 50, member B"
+ENSMUSG00000066189,SYMBOL,Cacng3
+ENSMUSG00000066189,GENENAME,"calcium channel, voltage-dependent, gamma subunit 3"
+ENSMUSG00000005611,SYMBOL,Irag1
+ENSMUSG00000005611,GENENAME,"inositol 1,4,5-triphosphate receptor associated 1"
+ENSMUSG00000064299,SYMBOL,4921528I07Rik
+ENSMUSG00000064299,GENENAME,RIKEN cDNA 4921528I07 gene
+ENSMUSG00000028174,SYMBOL,Rpe65
+ENSMUSG00000028174,GENENAME,retinal pigment epithelium 65
+ENSMUSG00000024902,SYMBOL,Mrpl11
+ENSMUSG00000024902,GENENAME,mitochondrial ribosomal protein L11

vignettes/data/GSE60450_metadata.csv

@@ -0,0 +1,13 @@
+gene_id,characteristics
+GSM1480291,mammary gland;luminal cells;virgin
+GSM1480292,mammary gland;luminal cells;virgin
+GSM1480293,mammary gland;luminal cells;18.5 day pregnancy
+GSM1480294,mammary gland;luminal cells;18.5 day pregnancy
+GSM1480295,mammary gland;luminal cells;2 day lactation
+GSM1480296,mammary gland;luminal cells;2 day lactation
+GSM1480297,mammary gland;basal cells;virgin
+GSM1480298,mammary gland;basal cells;virgin
+GSM1480299,mammary gland;basal cells;18.5 day pregnancy
+GSM1480300,mammary gland;basal cells;18.5 day pregnancy
+GSM1480301,mammary gland;basal cells;2 day lactation
+GSM1480302,mammary gland;basal cells;2 day lactation

vignettes/data/GSE60450_normalized_data.csv

@@ -0,0 +1,21 @@
+X,gene_symbol,GSM1480291,GSM1480292,GSM1480293,GSM1480294,GSM1480295,GSM1480296,GSM1480297,GSM1480298,GSM1480299,GSM1480300,GSM1480301,GSM1480302
+ENSMUSG00000031805,Jak3,82.22869,81.18604,36.13808,36.62751,12.35039,11.85235,10.59006,14.88337,7.57182,7.05763,3.16982,4.25451
+ENSMUSG00000033909,Usp36,88.2236,94.59098,76.11531,63.73863,27.10872,24.8705,95.67017,100.73912,78.0747,59.35009,36.36491,40.37057
+ENSMUSG00000065524,Mir135a-2,0,0,0,0,0,0,0,0,0,0,0,0
+ENSMUSG00000030374,Strn4,94.26324,85.05204,59.54855,54.30684,24.42892,24.90936,125.00263,102.99289,110.64124,97.9813,77.96883,105.70093
+ENSMUSG00000098547,Mir6921,0.08948,0.08404,0,0.08459,0.03884,0.07772,0,0.08505,0.07726,0.08255,0.04403,0.04727
+ENSMUSG00000035629,Rubcn,37.84846,37.73554,21.32397,27.70326,30.13807,36.33424,33.84822,36.91075,27.46715,31.36722,56.0002,64.33764
+ENSMUSG00000094053,Scgb2b7,0,0,0,0,0,0,0,0,0,0,0,0
+ENSMUSG00000055491,Pprc1,194.8793,165.14551,159.82546,167.99592,75.6947,82.42238,281.97525,241.83343,227.84988,232.81909,166.85593,150.56237
+ENSMUSG00000053080,2700081O15Rik,65.94401,78.91686,44.77617,35.69702,8.66081,9.98706,62.6212,61.82975,49.98944,42.01557,37.24541,40.08694
+ENSMUSG00000039715,Wdr34,18.20842,18.95181,11.60091,8.41671,3.72842,3.69171,17.98312,13.6927,9.00119,9.69908,10.38997,11.109
+ENSMUSG00000033475,Tomm6,53.46207,49.03939,50.827,49.95045,47.49852,46.04928,51.79137,49.49782,52.84819,47.00956,37.11334,35.97424
+ENSMUSG00000026283,Ing5,42.45649,45.46754,22.03338,22.45867,8.73849,11.114,50.07299,50.94364,45.04458,36.89776,44.28946,46.70506
+ENSMUSG00000037331,Larp1,260.82331,246.03739,230.05686,220.2303,128.98005,120.11673,147.58143,128.20957,168.08661,133.35197,100.02551,98.32645
+ENSMUSG00000074489,Bglap3,185.8422,188.25747,148.76704,163.80871,51.34346,48.84721,52.8304,84.66509,323.54064,485.86178,197.27742,163.89317
+ENSMUSG00000038246,Fam50b,0.04474,0,0,0,0.03884,0.03886,0.07992,0,0,0,0,0.09454
+ENSMUSG00000066189,Cacng3,0,0,0,0.0423,0,0,0,0,0.03863,0,0,0
+ENSMUSG00000005611,Mrvi1,0.67107,0.92448,0.29211,0.21148,0.38838,0.03886,102.26398,81.05056,115.31568,138.38724,177.99434,185.16572
+ENSMUSG00000064299,4921528I07Rik,0,0,0,0,0,0,0.03996,0,0,0,0,0
+ENSMUSG00000028174,Rpe65,0,0,0,0,0,0,0,0,0,0,0,0
+ENSMUSG00000024902,Mrpl11,27.60343,23.91038,21.86646,18.56753,11.8455,11.3083,14.02683,11.5665,12.13036,12.21671,10.21387,10.06901

vignettes/data/cms_hospital_patient_satisfaction.csv

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+ID,Facility Name,County,Hospital Type,Star Rating,No of Surveys,Response Rate,Overall Rating
+050424,SCRIPPS GREEN HOSPITAL,SAN DIEGO,Acute Care Hospital,4,3110,41,5
+140103,ST BERNARD HOSPITAL,COOK,Acute Care Hospital,1,264,6,2
+100051,SOUTH LAKE HOSPITAL,LAKE,Acute Care Hospital,2,1382,20,2
+040062,MERCY HOSPITAL FORT SMITH,SEBASTIAN,Acute Care Hospital,3,2506,35,3
+440048,BAPTIST MEMORIAL HOSPITAL,SHELBY,Acute Care Hospital,2,1799,18,2
+450011,ST JOSEPH REGIONAL HEALTH CENTER,BRAZOS,Acute Care Hospital,3,1379,24,3
+151317,GREENE COUNTY GENERAL HOSPITAL,GREENE,Critical Access Hospital,3,114,22,3
+061327,SOUTHWEST MEMORIAL HOSPITAL,MONTEZUMA,Critical Access Hospital,4,247,34,3
+490057,SENTARA GENERAL HOSPITAL,VIRGINIA BEACH,Acute Care Hospital,4,619,32,3
+110215,PIEDMONT FAYETTE HOSPITAL,FAYETTE,Acute Care Hospital,2,1714,21,2
+050704,MISSION COMMUNITY HOSPITAL,LOS ANGELES,Acute Care Hospital,3,241,14,3
+100296,DOCTORS HOSPITAL,MIAMI-DADE,Acute Care Hospital,4,393,24,3
+440003,SUMNER REGIONAL MEDICAL CENTER,SUMNER,Acute Care Hospital,4,680,35,2
+501339,WHIDBEY GENERAL HOSPITAL,ISLAND,Critical Access Hospital,3,389,29,3
+050116,NORTHRIDGE MEDICAL CENTER,LOS ANGELES,Acute Care Hospital,3,1110,20,2