SCPCP000006 - Add 01-clustering template analysis

analyses/cell-type-wilms-tumor-06/README.md

@@ -175,6 +175,19 @@ If you are using RStudio Server within the container, the `renv` project will no
 You can install packages within the container and use `renv::snapshot()` to update the lockfile without activating the project without a problem in our testing.
 The `renv` lockfile is used to install R packages in the Docker image.
 
+## Start the analysis
+
+Once you have (1) downloaded the data (See Input file section above) and (2) connect to your RStudio Session (See Docker section above) :
+
+you are READY TO START!
+
+Open the render_01-clustering.R file and render it to all samples in the dataset using [Source].
+
+html report will be created from the template notebook 01-clustering.Rmd.
+html reports can be found in notebook/01-clustering folder.
+
+
+
 ## Computational resources
 
 

analyses/cell-type-wilms-tumor-06/marker-sets/Pathway_metadata.csv

@@ -0,0 +1,5 @@
+pathway,category,subcategory,genes,URL
+HALLMARK_P53_PATHWAY,H,NA,"c(""ABAT"",""ABCC5"",""ABHD4"",""ACVR1B"",""ADA"",""COQ8A"",""AEN"",""AK1"",""ALOX15B"",""ANKRA2"",""APAF1"",""APP"",""ATF3"",""BAIAP2"",""BAK1"",""BAX"",""BLCAP"",""BMP2"",""BTG1"",""BTG2"",""CASP1"",""CCND2"",""CCND3"",""CCNG1"",""CCNK"",""CCP110"",""CD81"",""CD82"",""CDH13"",""CDK5R1"",""CDKN1A"",""CDKN2A"",""CDKN2AIP"",""CDKN2B"",""CEBPA"",""CGRRF1"",""CLCA2"",""CSRNP2"",""CTSD"",""CTSF"",""CYFIP2"",""DCXR"",""DDB2"",""DDIT3"",""DDIT4"",""DEF6"",""DGKA"",""DNTTIP2"",""DRAM1"",""EI24"",""EPHA2"",""EPHX1"",""EPS8L2"",""ERCC5"",""F2R"",""FAM162A"",""FAS"",""FBXW7"",""FDXR"",""FGF13"",""FOS"",""FOXO3"",""FUCA1"",""GADD45A"",""GLS2"",""GM2A"",""RACK1"",""GPX2"",""H2AJ"",""HBEGF"",""HDAC3"",""HEXIM1"",""HINT1"",""H1-2"",""H2AC25"",""HMOX1"",""HRAS"",""HSPA4L"",""IER3"",""IER5"",""IFI30"",""ELP1"",""IL1A"",""INHBB"",""IP6K2"",""IRAK1"",""ISCU"",""ITGB4"",""JAG2"",""JUN"",""KIF13B"",""KLF4"",""KLK8"",""KRT17"",""LDHB"",""LIF"",""IRAG2"",""MAPKAPK3"",""MDM2"",""MKNK2"",""MXD1"",""MXD4"",""NDRG1"",""NHLH2"",""NINJ1"",""NOL8"",""NOTCH1"",""NUDT15"",""NUPR1"",""OSGIN1"",""PCNA"",""PDGFA"",""PERP"",""PHLDA3"",""PIDD1"",""PITPNC1"",""PLK2"",""PLK3"",""PLXNB2"",""PMM1"",""POLH"",""POM121"",""PPM1D"",""PPP1R15A"",""PRKAB1"",""PRMT2"",""PROCR"",""PTPN14"",""PTPRE"",""PVT1"",""RAB40C"",""RAD51C"",""RAD9A"",""RALGDS"",""RAP2B"",""RB1"",""RCHY1"",""RETSAT"",""RGS16"",""RHBDF2"",""RNF19B"",""RPL18"",""RPL36"",""RPS12"",""RPS27L"",""RRAD"",""RRP8"",""RXRA"",""S100A10"",""S100A4"",""SAT1"",""SDC1"",""SEC61A1"",""SERPINB5"",""SERTAD3"",""SESN1"",""SFN"",""SLC19A2"",""SLC35D1"",""SLC3A2"",""SLC7A11"",""SOCS1"",""SP1"",""SPHK1"",""ST14"",""STEAP3"",""STOM"",""TAP1"",""TAX1BP3"",""TCHH"",""TCN2"",""TGFA"",""TGFB1"",""TM4SF1"",""TM7SF3"",""TNFSF9"",""TNNI1"",""TOB1"",""TP53"",""TP63"",""TPD52L1"",""TPRKB"",""TRAF4"",""TRAFD1"",""TRIAP1"",""TRIB3"",""TSC22D1"",""TSPYL2"",""TXNIP"",""UPP1"",""VAMP8"",""VDR"",""VWA5A"",""WRAP73"",""WWP1"",""XPC"",""ZBTB16"",""ZFP36L1"",""ZMAT3"",""ZNF365"")",https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_P53_PATHWAY
+HALLMARK_DNA_REPAIR,H,NA,"c(""AAAS"",""ADA"",""ADCY6"",""ADRM1"",""AK1"",""AK3"",""APRT"",""ARL6IP1"",""BCAM"",""BCAP31"",""BOLA2"",""BRF2"",""MPC2"",""CANT1"",""CCNO"",""CDA"",""CETN2"",""CLP1"",""CMPK2"",""NELFB"",""COX17"",""CSTF3"",""DAD1"",""DCTN4"",""DDB1"",""DDB2"",""GSDME"",""DGCR8"",""DGUOK"",""DUT"",""EDF1"",""EIF1B"",""AGO4"",""ELL"",""ERCC1"",""ERCC2"",""ERCC3"",""ERCC4"",""ERCC5"",""ERCC8"",""FEN1"",""GMPR2"",""GPX4"",""GTF2A2"",""GTF2B"",""GTF2F1"",""GTF2H1"",""GTF2H3"",""GTF2H5"",""GTF3C5"",""GUK1"",""HCLS1"",""HPRT1"",""IMPDH2"",""ITPA"",""LIG1"",""MPG"",""MRPL40"",""NCBP2"",""NFX1"",""NME1"",""NME3"",""NME4"",""NPR2"",""NT5C"",""NT5C3A"",""NUDT21"",""NUDT9"",""PCNA"",""PDE4B"",""PDE6G"",""PNP"",""POLA1"",""POLA2"",""POLB"",""POLD1"",""POLD3"",""POLD4"",""POLE4"",""POLH"",""POLL"",""POLR1C"",""POLR1D"",""POLR2A"",""POLR2C"",""POLR2D"",""POLR2E"",""POLR2F"",""POLR2G"",""POLR2H"",""POLR2I"",""POLR2J"",""POLR2K"",""POLR3C"",""POLR3GL"",""POM121"",""PRIM1"",""RAD51"",""RAD52"",""RAE1"",""RALA"",""RBX1"",""NELFE"",""REV3L"",""RFC2"",""RFC3"",""RFC4"",""RFC5"",""RNMT"",""RPA2"",""RPA3"",""RRM2B"",""SAC3D1"",""SDCBP"",""SEC61A1"",""SF3A3"",""SMAD5"",""SNAPC4"",""SNAPC5"",""SRSF6"",""SSRP1"",""STX3"",""SUPT4H1"",""SUPT5H"",""SURF1"",""TAF10"",""TAF12"",""TAF13"",""TAF1C"",""TAF6"",""TAF9"",""TARBP2"",""ELOA"",""NELFCD"",""ALYREF"",""TK2"",""TMED2"",""TP53"",""TSG101"",""TYMS"",""UMPS"",""UPF3B"",""USP11"",""VPS28"",""VPS37B"",""VPS37D"",""XPC"",""ZNF707"",""POLR1H"",""ZWINT"")",https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_DNA_REPAIR.html
+DROSHA_TARGET_GENES,C3,TFT:GTRD: GTRD,"c(""ABHD5"",""NSMAF"",""DNAJC25"",""NCKAP1"",""CLASP1"",""ARHGAP4"",""POLDIP3"",""ZNF175"",""PMPCB"",""KCNT1"",""TTC1"",""KDM3B"",""EGR1"",""MRPS2"",""AMD1"",""BCAS4"",""ARHGAP22"",""KNSTRN"",""TAF4"",""ALDH1L2"",""INTS15"",""PTGES2"",""UBALD1"",""BTG3"",""CXXC1"",""LSM11"",""PIERCE1"",""ANO10"",""DNAJB4"",""ZC3H12A"",""WDR41"",""ATG4B"",""ROR2"",""PLEKHF2"",""THAP4"",""SLC38A9"",""SRRM3"",""ADARB1"",""MTCO3P12"",""MT-ND2"",""MT-ND3"",""MT-ND1"",""MT-ATP6"",""MT-CO3"",""RNU5A-1"",""LRRC37A5P"",""RNVU1-15"",""MT-TL1"",""MT-TV"",""MT-RNR2"",""MT-TI"",""MT-TQ"",""MT-TM"",""MT-TS1"",""MT-TK"",""MT-TG"",""MT-ATP8"","""",""PTGES2-AS1"",""LINC01719"",""ZC3H12A-DT"",""SSR4P1"",""TMEM250"",""DNAJC25-GNG10"",""MTND5P11"",""MALAT1"","""","""",""MIR3190"","""",""RNU11"",""RNVU1-19"")",https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/DROSHA_TARGET_GENES.html
+DICER1_TARGET_GENES,C3,TFT:GTRD: GTRD,"c(""STRAP"",""LRP6"",""HNRNPH3"",""SCD"",""MED15"",""TFIP11"",""POLDIP3"",""SNX16"",""EIF3B"",""ITFG2"",""NAA25"",""NOP2"",""NCOA7"",""RPL24"",""PLCH1"",""NDUFS7"",""C2orf42"",""TIA1"",""GADD45A"",""COQ6"",""RPL5"",""KLHL7"",""NAGK"",""WDR74"",""MYO18B"",""EMP1"",""FCHSD2"",""KNL1"",""BCAR3"",""YARS2"",""POLG"",""MTF2"",""ILF2"",""NDUFB9"",""TATDN1"",""C9orf72"",""PAMR1"",""PFKM"",""CCDC107"",""DUSP19"",""SP2"",""HSPA6"",""MGA"",""MED16"",""TMEM39A"",""CCDC43"",""TMEM259"",""KLHL32"",""RNF216P1"",""KIAA1671"",""MT-ND6"",""MTCO3P12"",""MT-ND2"",""MT-ATP6"",""RNU5E-1"","""",""RNU5B-1"",""SNORD118"",""RNVU1-6"",""RNU4-2"",""MT-TF"",""MT-TI"",""MT-TM"",""MT-TS1"",""MT-TK"",""MT-TE"",""MT-TT"",""MT-TP"",""MT-RNR1"","""",""ZBTB9"",""ANG"",""NBPF1"",""RNU2-2P"",""RN7SKP264"",""HCG14"",""MT-ATP8"",""KLHL7-DT"","""",""LINC01719"",""HBB"",""ITFG2-AS1"",""ITFG2-AS1"",""RNASE4"",""TFIP11-DT"",""POLG-DT"",""SNORD3A"",""SP2-DT"","""","""","""",""RNVU1-29"",""SYNGAP1-AS1"",""RNU12"",""FRG1HP"",""H4C5"",""SCARNA2"",""H4C2"")",https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/DICER1_TARGET_GENES