Using haploR, an R package for querying HaploReg, RegulomeDB and LDlink

#library(knitcitations)
#cleanbib()
#options("citation_format" = "pandoc")
#r<-citep("10.1093/nar/gkr917") 
#r<-citep("10.1101/gr.137323.112")
#r<-citep("10.1093/bioinformatics/btv402")
#write.bibtex(file="references.bib")

Overview

HaploReg (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) [@Ward_2011], RegulomeDB (http://www.regulomedb.org) [@Boyle_2012], and LDlink (https://analysistools.nci.nih.gov/LDlink/) [@Machiela_2015] are web-based tools that extract biological information such as eQTL, LD, LD matrices, motifs, etc. from large genomic projects such as ENCODE, the 1000 Genomes Project, Roadmap Epigenomics Project and others. This is sometimes called "post stage GWAS" analysis.

The R-package haploR was developed to query those tools (HaploReg, RegulomeDB, LDlink) directly from R in order to facilitate high-throughput genomic data analysis. Below we provide several examples that show how to work with this package.

Note: you must have a stable Internet connection to use this package.

Contact: ilya.zhbannikov@duke.edu for questions of usage the haploR or any other issues.

Motivation and typical analysis workflow

This package was inspired by the fact that many web-based post stage GWAS databases do not have Application Programing Interface (API) and, therefore, do not allow users to query them remotedly from R environment. In our research we used HaploReg and RegulomeDB web databases. These very useful web databases show information about linkage disequilibrium of query variants and variants which are in LD with them, expression quantitative trait loci (eQTL), motifs changed and other useful information. However, it is not easy to include this information into streamlined workflow since those tools also not offer API.

We developed a custom analysis pipeline which prepares data, performs genome-wide association (GWA) analysis and presents results in a user-friendly format. Results include a list of genetic variants (also known as 'SNP' or single nucleotide polymorphism), their corresponding p-values, phenotypes (traits) tested and other meta-information such as LD, alternative allele, minor allele frequency, motifs changed, etc. Of course, we could go throught the list of SNPs having genome-wide significant p-values (1e-8) and submit each of those SNPs to web-based tools manually, one-by-one, but it is time-consuming process and will not be fully automatic (which ruins one of the pipeline's paradigms). This is especially difficult if the web site does not offer downloading results.

Therefore, we developed haploR, a user-friendly R package that connects to the web tool from R environment with methods POST/GET and downloads results in a suitable R format. This package siginificantly saved our time in developing reporting system for our internal genomic analysis pipeline and now we would like to present haploR to the research community.

Example of typical analysis workflow is shown below.

Typical analysis workflow

Installation of haploR package

In order to install the haploR package, the user must first install R (https://www.r-project.org). After that, haploR can be installed either:

install.packages("haploR", dependencies = TRUE)
devtools::install_github("izhbannikov/haplor")

haploR depends on the following packages:

Examples of usage

Querying HaploReg

Function

queryHaploreg(query = NULL, file = NULL, study = NULL, ldThresh = 0.8,
  ldPop = "EUR", epi = "vanilla", cons = "siphy", genetypes = "gencode",
  url = "https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php",
  timeout = 10, encoding = "UTF-8", verbose = FALSE)

queries HaploReg web-based tool and returns results.

Arguments

Output

A data frame (table) wrapped into a tibble object contains data extracted from HaploReg site. The colums (33 in total at the time of writing this vignette) are specific to HaploReg output. Below we describe the columns:

Number of rows is not constant, at least equal or more than the number of query SNPs, and depends on r2 parameter choosen in a query (default 0.8). This means that the program outputs not only query SNPs, but also those SNPs that have r2 $\geq$ 0.8 with the query SNPs.

One or several genetic variants

library(haploR)
x <- queryHaploreg(query=c("rs10048158","rs4791078"))
x

Here query is a vector with names of genetic variants.

We then can create a subset from the results, for example, to choose only SNPs with r2 $>$ 0.9:

subset.high.LD <- x[as.numeric(x$r2) > 0.9, c("rsID", "r2", "chr", "pos_hg38", "is_query_snp", "ref", "alt")]
subset.high.LD

We can then save the subset.high.LD into an Excel workbook:

require(openxlsx)
write.xlsx(x=subset.high.LD, file="subset.high.LD.xlsx")

This was an example of gathering post-gwas information directly from the online tool. haploR has an additional advantage because it downloads the full information for query retrieved by HaploReg. For example, if you go online and submit these two SNPs to HaploReg (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php), you will see that some cells of columns "Motifs changed" and "Selected eQTL hits" are hidded (only number of hits are given). haploR retrives this information in a form of a data frame which can be saved into Excel file.

x[, c("Motifs", "rsID")]
x[, c("eQTL", "rsID")]

Uploading file with variants

If you have a file with your SNPs you would like to analyze, you can supply it as an input as follows:

library(haploR)
x <- queryHaploreg(file=system.file("extdata/snps.txt", package = "haploR"))
x

File "snps.txt" is a text file which contains one rs-ID per line:

rs10048158
rs4791078

Using existing studies

Sometimes one would like to explore results from already performed study. In this case you should first explore the existing studies from HaploReg web site (https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) and then use one of them as an input parameter. See example below:

library(haploR)
# Getting a list of existing studies:
studies <- getStudyList()
# Let us look at the first element:
studies[[1]]
# Let us look at the second element:
studies[[2]]
# Query Hploreg to explore results from 
# this study:
x <- queryHaploreg(study=studies[[1]])
x

Extended view of SNP

If you want to see more information about SNP of interest, you can use the getExtendedView: Parameters: snp - A SNP of interest. url - A url to the HaploReg. Default: "https://pubs.broadinstitute.org/mammals/haploreg/detail_v4.1.php?query=&id="

Return A list of tables t1, t2, ..., etc, depending on information contained in HaploReg database.

Example:

library(haploR)
tables <- getExtendedView(snp="rs10048158")
tables

Querying RegulomeDB

To query RegulomeDB use this function:

queryRegulome(query = NULL, 
              format = "full",
              url = "http://www.regulomedb.org/results", 
              timeout = 10,
              check_bad_snps = TRUE, 
              verbose = FALSE)

This function queries RegulomeDB http://www.regulomedb.org web-based tool and returns results in a named list.

Arguments

Output

A list of two: (1) a data frame (res.table) wrapped to a tibble object and (2) a list of bad SNP IDs (bad.snp.id). Bad SNP ID are those IDs that were not found in 1000 Genomes Phase 1 data and, therefore, in RegulomeDB.

Columns in a data frame (res.table):

Number of rows is equal or less (in case if not all SNPs were found in RegulomeDB database) to number of query SNPs.

All the information retreived from RegulomeDB, except hits, are also presented in HaploReg output (queryHaploReg(...)).

Example

library(haploR)
x <- queryRegulome(c("rs4791078","rs10048158"))
x$res.table
x$bad.snp.id

Querying LDlink

LDlink (https://analysistools.nci.nih.gov/LDlink/) is a set of web-based tools that allow exloring Linkage Disequilibrium of provided set of SNPs. LDlink allows for the following tools:

Currently haploR supports LDmatrix only but we are currently working on adding other tools from LDlink project.

LDmatrix

Function

LDlink.LDmatrix(snps, r2d = "r2", population = "ALL")

This function queries HaploReg web-based tool and returns results.

Arguments
Value

A list of two: (1) raw LD r2 matrix, (2) raw LD D-prime matrix.

Example
library(haploR)
ldmat <- LDlink.LDmatrix(snps=c("rs77264218", "rs11229158", "rs10896659", "rs10896702", "rs2042592"), population="AFR")
ldmat
# Stylish matrix R2
stylish.matrix.r2 <- makeStylishLDmatrix(ldmat$matrix.r2)
stylish.matrix.r2
# Stylish matrix D'
stylish.matrix.Dprime <- makeStylishLDmatrix(ldmat$matrix.dprime)
stylish.matrix.Dprime

Roadmap cell types

The Roadmap Epigenomics project employs data organization schema based on anatomical origin of the data (see Roadmap Epigenomics web site).

| EID | GROUP | ANATOMY | GR | Epigenome Mnemonic | Standardized Epigenome name (from Wouter) | Epigenome name (from EDACC Release 9 directory) | TYPE | |------|----------------|--------------------|-----------------|----------------------------|----------------------------------------------------------------|----------------------------------------------------------------------------|----------------| | E033 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD3.CPC | Primary T cells from cord blood | CD3_Primary_Cells_Cord_BI | PrimaryCell | | E034 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD3.PPC | Primary T cells from peripheral blood | CD3_Primary_Cells_Peripheral_UW | PrimaryCell | | E037 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.MPC | Primary T helper memory cells from peripheral blood 2 | CD4_Memory_Primary_Cells | PrimaryCell | | E038 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.NPC | Primary T helper naive cells from peripheral blood | CD4_Naive_Primary_Cells | PrimaryCell | | E039 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25M.CD45RA.NPC | Primary T helper naive cells from peripheral blood | CD4+_CD25-_CD45RA+_Naive_Primary_Cells | PrimaryCell | | E040 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25M.CD45RO.MPC | Primary T helper memory cells from peripheral blood 1 | CD4+_CD25-_CD45RO+_Memory_Primary_Cells | PrimaryCell | | E041 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25M.IL17M.PL.TPC | Primary T helper cells PMA-I stimulated | CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells
| PrimaryCell | | E042 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25M.IL17P.PL.TPC | Primary T helper 17 cells PMA-I stimulated | CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells | PrimaryCell | | E043 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25M.TPC | Primary T helper cells from peripheral blood | CD4+_CD25-_Th_Primary_Cells | PrimaryCell | | E044 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25.CD127M.TREGPC | Primary T regulatory cells from peripheral blood | CD4+_CD25+_CD127-_Treg_Primary_Cells | PrimaryCell | | E045 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD4.CD25I.CD127.TMEMPC | Primary T cells effector/memory enriched from peripheral blood | CD4+_CD25int_CD127+_Tmem_Primary_Cells | PrimaryCell | | E047 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD8.NPC | Primary T CD8+ naive cells from peripheral blood | CD8_Naive_Primary_Cells | PrimaryCell | | E048 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.CD8.MPC | Primary T CD8+ memory cells from peripheral blood | CD8_Memory_Primary_Cells | PrimaryCell | | E062 | Blood & T-cell | BLOOD | Blood_and_Tcell | BLD.PER.MONUC.PC | Primary mononuclear cells from peripheral blood | Peripheral_Blood_Mononuclear_Primary_Cells | PrimaryCell | | E053 | Neurosph | BRAIN | Brain | BRN.CRTX.DR.NRSPHR | Cortex derived primary cultured neurospheres | Neurosphere_Cultured_Cells_Cortex_Derived | PrimaryCulture | | E054 | Neurosph | BRAIN | Brain | BRN.GANGEM.DR.NRSPHR | Ganglion Eminence derived primary cultured neurospheres | Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived | PrimaryCulture | | E067 | Brain | BRAIN | Brain | BRN.ANG.GYR | Brain Angular Gyrus | Brain_Angular_Gyrus | PrimaryTissue | | E068 | Brain | BRAIN | Brain | BRN.ANT.CAUD | Brain Anterior Caudate | Brain_Anterior_Caudate | PrimaryTissue | | E069 | Brain | BRAIN | Brain | BRN.CING.GYR | Brain Cingulate Gyrus | Brain_Cingulate_Gyrus | PrimaryTissue | | E070 | Brain | BRAIN | Brain | BRN.GRM.MTRX | Brain Germinal Matrix | Brain_Germinal_Matrix | PrimaryTissue | | E071 | Brain | BRAIN | Brain | BRN.HIPP.MID | Brain Hippocampus Middle | Brain_Hippocampus_Middle | PrimaryTissue | | E072 | Brain | BRAIN | Brain | BRN.INF.TMP | Brain Inferior Temporal Lobe | Brain_Inferior_Temporal_Lobe | PrimaryTissue | | E073 | Brain | BRAIN | Brain | BRN.DL.PRFRNTL.CRTX | Brain_Dorsolateral_Prefrontal_Cortex | Brain_Mid_Frontal_Lobe | PrimaryTissue | | E074 | Brain | BRAIN | Brain | BRN.SUB.NIG | Brain Substantia Nigra | Brain_Substantia_Nigra | PrimaryTissue | | E081 | Brain | BRAIN | Brain | BRN.FET.M | Fetal Brain Male | Fetal_Brain_Male | PrimaryTissue | | E082 | Brain | BRAIN | Brain | BRN.FET.F | Fetal Brain Female | Fetal_Brain_Female | PrimaryTissue | | E075 | Digestive | GI_COLON | Digestive | GI.CLN.MUC | Colonic Mucosa | Colonic_Mucosa | PrimaryTissue | | E077 | Digestive | GI_DUODENUM | Digestive | GI.DUO.MUC | Duodenum Mucosa | Duodenum_Mucosa | PrimaryTissue | | E079 | Digestive | GI_ESOPHAGUS | Digestive | GI.ESO | Esophagus | Esophagus | PrimaryTissue | | E084 | Digestive | GI_INTESTINE | Digestive | GI.L.INT.FET | Fetal Intestine Large | Fetal_Intestine_Large | PrimaryTissue | | E085 | Digestive | GI_INTESTINE | Digestive | GI.S.INT.FET | Fetal Intestine Small | Fetal_Intestine_Small | PrimaryTissue | | E092 | Digestive | GI_STOMACH | Digestive | GI.STMC.FET | Fetal Stomach | Fetal_Stomach | PrimaryTissue | | E094 | Digestive | GI_STOMACH | Digestive | GI.STMC.GAST | Gastric | Gastric | PrimaryTissue | | E101 | Digestive | GI_RECTUM | Digestive | GI.RECT.MUC.29 | Rectal Mucosa Donor 29 | Rectal_Mucosa.Donor_29 | PrimaryTissue | | E102 | Digestive | GI_RECTUM | Digestive | GI.RECT.MUC.31 | Rectal Mucosa Donor 31 | Rectal_Mucosa.Donor_31 | PrimaryTissue | | E106 | Digestive | GI_COLON | Digestive | GI.CLN.SIG | Sigmoid Colon | Sigmoid_Colon | PrimaryTissue | | E109 | Digestive | GI_INTESTINE | Digestive | GI.S.INT | Small Intestine | Small_Intestine | PrimaryTissue | | E110 | Digestive | GI_STOMACH | Digestive | GI.STMC.MUC | Stomach Mucosa | Stomach_Mucosa | PrimaryTissue | | E114 | ENCODE2012 | LUNG | ENCODE2012 | LNG.A549.ETOH002.CNCR | A549 EtOH 0.02pct Lung Carcinoma Cell Line | A549_EtOH_0.02pct_Lung_Carcinoma | CellLine | | E115 | ENCODE2012 | BLOOD | ENCODE2012 | BLD.DND41.CNCR | Dnd41 TCell Leukemia Cell Line | Dnd41_TCell_Leukemia | CellLine | | E116 | ENCODE2012 | BLOOD | ENCODE2012 | BLD.GM12878 | GM12878 Lymphoblastoid Cells | GM12878_Lymphoblastoid | PrimaryCulture | | E117 | ENCODE2012 | CERVIX | ENCODE2012 | CRVX.HELAS3.CNCR | HeLa-S3 Cervical Carcinoma Cell Line | HeLa-S3_Cervical_Carcinoma | CellLine | | E118 | ENCODE2012 | LIVER | ENCODE2012 | LIV.HEPG2.CNCR | HepG2 Hepatocellular Carcinoma Cell Line | HepG2_Hepatocellular_Carcinoma | CellLine | | E119 | ENCODE2012 | BREAST | ENCODE2012 | BRST.HMEC | HMEC Mammary Epithelial Primary Cells | HMEC_Mammary_Epithelial | PrimaryCulture | | E120 | ENCODE2012 | MUSCLE | ENCODE2012 | MUS.HSMM | HSMM Skeletal Muscle Myoblasts Cells | HSMM_Skeletal_Muscle_Myoblasts | PrimaryCulture | | E121 | ENCODE2012 | MUSCLE | ENCODE2012 | MUS.HSMMT | HSMM cell derived Skeletal Muscle Myotubes Cells | HSMMtube_Skeletal_Muscle_Myotubes_Derived_from_HSMM | PrimaryCulture | | E122 | ENCODE2012 | VASCULAR | ENCODE2012 | VAS.HUVEC | HUVEC Umbilical Vein Endothelial Primary Cells | HUVEC_Umbilical_Vein_Endothelial_Cells | PrimaryCulture | | E123 | ENCODE2012 | BLOOD | ENCODE2012 | BLD.K562.CNCR | K562 Leukemia Cells | K562_Leukemia | PrimaryCulture | | E124 | ENCODE2012 | BLOOD | ENCODE2012 | BLD.CD14.MONO | Monocytes-CD14+ RO01746 Primary Cells | Monocytes-CD14+_RO01746 | PrimaryCell | | E125 | ENCODE2012 | BRAIN | ENCODE2012 | BRN.NHA | NH-A Astrocytes Primary Cells | NH-A_Astrocytes | PrimaryCulture | | E126 | ENCODE2012 | SKIN | ENCODE2012 | SKIN.NHDFAD | NHDF-Ad Adult Dermal Fibroblast Primary Cells | NHDF-Ad_Adult_Dermal_Fibroblasts | PrimaryCulture | | E127 | ENCODE2012 | SKIN | ENCODE2012 | SKIN.NHEK | NHEK-Epidermal Keratinocyte Primary Cells | NHEK-Epidermal_Keratinocytes | PrimaryCulture | | E128 | ENCODE2012 | LUNG | ENCODE2012 | LNG.NHLF | NHLF Lung Fibroblast Primary Cells | NHLF_Lung_Fibroblasts | PrimaryCulture | | E129 | ENCODE2012 | BONE | ENCODE2012 | BONE.OSTEO | Osteoblast Primary Cells | Osteoblasts | PrimaryCulture | | E027 | Epithelial | BREAST | Epithelial | BRST.MYO | Breast Myoepithelial Primary Cells | Breast_Myoepithelial_Cells | PrimaryCell | | E028 | Epithelial | BREAST | Epithelial | BRST.HMEC.35 | Breast variant Human Mammary Epithelial Cells (vHMEC) | Breast_vHMEC | PrimaryCulture | | E055 | Epithelial | SKIN | Epithelial | SKIN.PEN.FRSK.FIB.01 | Foreskin Fibroblast Primary Cells skin01 | Penis_Foreskin_Fibroblast_Primary_Cells_skin01 | PrimaryCulture | | E056 | Epithelial | SKIN | Epithelial | SKIN.PEN.FRSK.FIB.02 | Foreskin Fibroblast Primary Cells skin02 | Penis_Foreskin_Fibroblast_Primary_Cells_skin02 | PrimaryCulture | | E057 | Epithelial | SKIN | Epithelial | SKIN.PEN.FRSK.KER.02 | Foreskin Keratinocyte Primary Cells skin02 | Penis_Foreskin_Keratinocyte_Primary_Cells_skin02 | PrimaryCulture | | E058 | Epithelial | SKIN | Epithelial | SKIN.PEN.FRSK.KER.03 | Foreskin Keratinocyte Primary Cells skin03 | Penis_Foreskin_Keratinocyte_Primary_Cells_skin03 | PrimaryCulture | | E059 | Epithelial | SKIN | Epithelial | SKIN.PEN.FRSK.MEL.01 | Foreskin Melanocyte Primary Cells skin01 | Penis_Foreskin_Melanocyte_Primary_Cells_skin01 | PrimaryCulture | | E061 | Epithelial | SKIN | Epithelial | SKIN.PEN.FRSK.MEL.03 | Foreskin Melanocyte Primary Cells skin03 | Penis_Foreskin_Melanocyte_Primary_Cells_skin03 | PrimaryCulture | | E004 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.H1.BMP4.MESO | H1 BMP4 Derived Mesendoderm Cultured Cells | H1_BMP4_Derived_Mesendoderm_Cultured_Cells | ESCDerived | | E005 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.H1.BMP4.TROP | H1 BMP4 Derived Trophoblast Cultured Cells | H1_BMP4_Derived_Trophoblast_Cultured_Cells | ESCDerived | | E006 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.H1.MSC | H1 Derived Mesenchymal Stem Cells | H1_Derived_Mesenchymal_Stem_Cells | ESCDerived | | E007 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.H1.NEUR.PROG | H1 Derived Neuronal Progenitor Cultured Cells | H1_Derived_Neuronal_Progenitor_Cultured_Cells | ESCDerived | | E009 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.H9.NEUR.PROG | H9 Derived Neuronal Progenitor Cultured Cells | H9_Derived_Neuronal_Progenitor_Cultured_Cells | ESCDerived | | E010 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.H9.NEUR | H9 Derived Neuron Cultured Cells | H9_Derived_Neuron_Cultured_Cells | ESCDerived | | E011 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.CD184.ENDO | hESC Derived CD184+ Endoderm Cultured Cells | hESC_Derived_CD184+_Endoderm_Cultured_Cells | ESCDerived | | E012 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.CD56.ECTO | hESC Derived CD56+ Ectoderm Cultured Cells | hESC_Derived_CD56+_Ectoderm_Cultured_Cells | ESCDerived | | E013 | ES-deriv | ESC_DERIVED | ES-deriv | ESDR.CD56.MESO | hESC Derived CD56+ Mesoderm Cultured Cells | hESC_Derived_CD56+_Mesoderm_Cultured_Cells | ESCDerived | | E001 | ESC | ESC | ESC | ESC.I3 | ES-I3 Cells | ES-I3_Cell_Line | PrimaryCulture | | E002 | ESC | ESC | ESC | ESC.WA7 | ES-WA7 Cells | ES-WA7_Cell_Line | PrimaryCulture | | E003 | ESC | ESC | ESC | ESC.H1 | H1 Cells | H1_Cell_Line | PrimaryCulture | | E008 | ESC | ESC | ESC | ESC.H9 | H9 Cells | H9_Cell_Line | PrimaryCulture | | E014 | ESC | ESC | ESC | ESC.HUES48 | HUES48 Cells | HUES48_Cell_Line | PrimaryCulture | | E015 | ESC | ESC | ESC | ESC.HUES6 | HUES6 Cells | HUES6_Cell_Line | PrimaryCulture | | E016 | ESC | ESC | ESC | ESC.HUES64 | HUES64 Cells | HUES64_Cell_Line | PrimaryCulture | | E024 | ESC | ESC | ESC | ESC.4STAR | ES-UCSF4 Cells | 4star | PrimaryCulture | | E065 | Heart | VASCULAR | Heart | VAS.AOR | Aorta | Aorta | PrimaryTissue | | E083 | Heart | HEART | Heart | HRT.FET | Fetal Heart | Fetal_Heart | PrimaryTissue | | E095 | Heart | HEART | Heart | HRT.VENT.L | Left Ventricle | Left_Ventricle | PrimaryTissue | | E104 | Heart | HEART | Heart | HRT.ATR.R | Right Atrium | Right_Atrium | PrimaryTissue | | E105 | Heart | HEART | Heart | HRT.VNT.R | Right Ventricle | Right_Ventricle | PrimaryTissue | | E029 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD14.PC | Primary monocytes from peripheral blood | CD14_Primary_Cells | PrimaryCell | | E030 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD15.PC | Primary neutrophils from peripheral blood | CD15_Primary_Cells | PrimaryCell | | E031 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD19.CPC | Primary B cells from cord blood | CD19_Primary_Cells_Cord_BI | PrimaryCell | | E032 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD19.PPC | Primary B cells from peripheral blood | CD19_Primary_Cells_Peripheral_UW | PrimaryCell | | E035 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD34.PC | Primary hematopoietic stem cells | CD34_Primary_Cells | PrimaryCell | | E036 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD34.CC | Primary hematopoietic stem cells short term culture | CD34_Cultured_Cells | PrimaryCell | | E046 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.CD56.PC | Primary Natural Killer cells from peripheral blood | CD56_Primary_Cells | PrimaryCell | | E050 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.MOB.CD34.PC.F | Primary hematopoietic stem cells G-CSF-mobilized Female | Mobilized_CD34_Primary_Cells_Female | PrimaryCell | | E051 | HSC & B-cell | BLOOD | HSC_and_Bcell | BLD.MOB.CD34.PC.M | Primary hematopoietic stem cells G-CSF-mobilized Male | Mobilized_CD34_Primary_Cells_Male | PrimaryCell | | E018 | iPSC | IPSC | iPSC | IPSC.15b | iPS-15b Cells | iPS-15b_Cell_Line | PrimaryCulture | | E019 | iPSC | IPSC | iPSC | IPSC.18 | iPS-18 Cells | iPS-18_Cell_Line | PrimaryCulture | | E020 | iPSC | IPSC | iPSC | IPSC.20B | iPS-20b Cells | iPS-20b_Cell_Line | PrimaryCulture | | E021 | iPSC | IPSC | iPSC | IPSC.DF.6.9 | iPS DF 6.9 Cells | iPS_DF_6.9_Cell_Line | PrimaryCulture | | E022 | iPSC | IPSC | iPSC | IPSC.DF.19.11 | iPS DF 19.11 Cells | iPS_DF_19.11_Cell_Line | PrimaryCulture | | E023 | Mesench | FAT | Mesench | FAT.MSC.DR.ADIP | Mesenchymal Stem Cell Derived Adipocyte Cultured Cells | Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells | PrimaryCulture | | E025 | Mesench | FAT | Mesench | FAT.ADIP.DR.MSC | Adipose Derived Mesenchymal Stem Cell Cultured Cells | Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells | PrimaryCulture | | E026 | Mesench | STROMAL_CONNECTIVE | Mesench | STRM.MRW.MSC | Bone Marrow Derived Cultured Mesenchymal Stem Cells | Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells | PrimaryCulture | | E049 | Mesench | STROMAL_CONNECTIVE | Mesench | STRM.CHON.MRW.DR.MSC | Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells | Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells | PrimaryCulture | | E052 | Myosat | MUSCLE | Muscle | MUS.SAT | Muscle Satellite Cultured Cells | Muscle_Satellite_Cultured_Cells | PrimaryCulture | | E089 | Muscle | MUSCLE | Muscle | MUS.TRNK.FET | Fetal Muscle Trunk | Fetal_Muscle_Trunk | PrimaryTissue | | E090 | Muscle | MUSCLE_LEG | Muscle | MUS.LEG.FET | Fetal Muscle Leg | Fetal_Muscle_Leg | PrimaryTissue | | E100 | Muscle | MUSCLE | Muscle | MUS.PSOAS | Psoas Muscle | Psoas_Muscle | PrimaryTissue | | E107 | Muscle | MUSCLE | Muscle | MUS.SKLT.M | Skeletal Muscle Male | Skeletal_Muscle_Male | PrimaryTissue | | E108 | Muscle | MUSCLE | Muscle | MUS.SKLT.F | Skeletal Muscle Female | Skeletal_Muscle_Female | PrimaryTissue | | E017 | IMR90 | LUNG | Other | LNG.IMR90 | IMR90 fetal lung fibroblasts Cell Line | IMR90_Cell_Line | CellLine | | E063 | Adipose | FAT | Other | FAT.ADIP.NUC | Adipose Nuclei | Adipose_Nuclei | PrimaryTissue | | E066 | Other | LIVER | Other | LIV.ADLT | Liver | Adult_Liver | PrimaryTissue | | E076 | Sm. Muscle | GI_COLON | Other | GI.CLN.SM.MUS | Colon Smooth Muscle | Colon_Smooth_Muscle | PrimaryTissue | | E078 | Sm. Muscle | GI_DUODENUM | Other | GI.DUO.SM.MUS | Duodenum Smooth Muscle | Duodenum_Smooth_Muscle | PrimaryTissue | | E080 | Other | ADRENAL | Other | ADRL.GLND.FET | Fetal Adrenal Gland | Fetal_Adrenal_Gland | PrimaryTissue | | E086 | Other | KIDNEY | Other | KID.FET | Fetal Kidney | Fetal_Kidney | PrimaryTissue | | E087 | Other | PANCREAS | Other | PANC.ISLT | Pancreatic Islets | Pancreatic_Islets | PrimaryTissue | | E088 | Other | LUNG | Other | LNG.FET | Fetal Lung | Fetal_Lung | PrimaryTissue | | E091 | Other | PLACENTA | Other | PLCNT.FET | Placenta | Fetal_Placenta | PrimaryTissue | | E093 | Thymus | THYMUS | Other | THYM.FET | Fetal Thymus | Fetal_Thymus | PrimaryTissue | | E096 | Other | LUNG | Other | LNG | Lung | Lung | PrimaryTissue | | E097 | Other | OVARY | Other | OVRY | Ovary | Ovary | PrimaryTissue | | E098 | Other | PANCREAS | Other | PANC | Pancreas | Pancreas | PrimaryTissue | | E099 | Other | PLACENTA | Other | PLCNT.AMN | Placenta Amnion | Placenta_Amnion | PrimaryTissue | | E103 | Sm. Muscle | GI_RECTUM | Other | GI.RECT.SM.MUS | Rectal Smooth Muscle | Rectal_Smooth_Muscle | PrimaryTissue | | E111 | Sm. Muscle | GI_STOMACH | Other | GI.STMC.MUS | Stomach Smooth Muscle | Stomach_Smooth_Muscle | PrimaryTissue | | E112 | Thymus | THYMUS | Other | THYM | Thymus | Thymus | PrimaryTissue | | E113 | Other | SPLEEN | Other | SPLN | Spleen | Spleen | PrimaryTissue |

Session information

sessionInfo()

References



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haploR documentation built on Jan. 19, 2019, 5:08 p.m.