diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..5b6a065
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..09d2f5f
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,27 @@
+Package: microsig
+Type: Package
+Title: Calculates Microbe Signature Score
+Version: 0.0.0.9000
+Authors@R: 
+    c(person(given = "Caroline",
+           family = "Wheeler",
+           role = c("aut"),
+           comment = c(ORCID = "0000-0002-3374-4909")),
+      person(given = "Rebecca", 
+            family = "Hoyd",
+            role = c("aut"),
+           comment = c(ORCID = "0000-0003-1210-4491")),
+      person(given = "Daniel",
+           family = "Spakowicz",
+           role = c("aut", "cre"),
+           email = "daniel.spakowicz@osumc.edu",
+           comment = c(ORCID = "0000-0003-2314-6435"))
+Maintainer: Daniel Spakowicz <daniel.spakowicz@osumc.edu>
+Description: This package contains functions to calculate microbe signatures, particularly from bugsigdb inputs. 
+License: MIT
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Imports: 
+    dplyr,
+    tidyr
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..d0bd7d7
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,7 @@
+# Generated by roxygen2: do not edit by hand
+
+export(calcMicroSigScore)
+export(getSigList)
+export(microbeEntries)
+import(dplyr)
+import(tidyr)
diff --git a/R/calcMicroSigScore.R b/R/calcMicroSigScore.R
new file mode 100644
index 0000000..c7142a3
--- /dev/null
+++ b/R/calcMicroSigScore.R
@@ -0,0 +1,58 @@
+#' Function to calculate microbe signature scores given a set of up and down
+#' regulated microbes and the relative abundances of microbe per sample
+#'
+#' @param taxa a data frame where columns are microbes and rows are samples, first
+#'    column named 'sample'
+#' @param sig.up a character vector listing microbes in given signature that are
+#'    up-regulated, empty if none
+#' @param sig.down a character vector listing microbes in given signature that are
+#'    down-regulated, empty if none
+#'
+#' @return a data frame with samples and corresponding microbe signature scores
+#'
+#' @import dplyr
+#' @import tidyr
+#'
+#' @export
+calcMicroSigScore <- function(taxa, sig.up, sig.down){
+  df <- taxa %>%
+    tidyr::gather(microbe, exo.ra, -sample) %>%
+    dplyr::group_by(sample) %>%
+    dplyr::mutate(z_score = scale(exo.ra))
+
+  upMics <- df %>%
+    dplyr::filter(microbe %in% sig.up)
+
+  upTotal <- length(unique(upMics$microbe))
+
+  upMics <- upMics %>%
+    dplyr::group_by(sample) %>%
+    dplyr::summarize(tempUp = sum(exo.ra))
+
+  downMics <- df %>%
+    dplyr::filter(microbe %in% sig.down)
+
+  downTotal <- length(unique(downMics$microbe))
+
+  downMics <- downMics %>%
+    dplyr::group_by(sample) %>%
+    dplyr::summarize(tempDown = sum(exo.ra))
+
+  if(upTotal == 0 && downTotal == 0){
+    df <- data.frame(matrix(ncol = 0, nrow = 0))
+  }else if(upTotal == 0){
+    df <- downMics %>%
+      dplyr::mutate(score = tempDown*(1/downTotal)) %>%
+      dplyr::select(sample,score)
+  }else if(downTotal == 0){
+    df <- upMics %>%
+      dplyr::mutate(score = tempUp*(1/upTotal)) %>%
+      dplyr::select(sample, score)
+  }else{
+    df <- merge(upMics, downMics, by = "sample") %>%
+      dplyr::mutate(score = (tempUp - tempDown)*(1/(upTotal + downTotal))) %>%
+      dplyr::select(sample, score)
+  }
+
+  return(df)
+}
diff --git a/R/getSigList.R b/R/getSigList.R
new file mode 100644
index 0000000..37a1e5d
--- /dev/null
+++ b/R/getSigList.R
@@ -0,0 +1,14 @@
+#' Given a single cell value from bigsigDB output in the column 'MetaPhlAn.taxon.names',
+#' returns a list of the microbes
+#'
+#' @param sig character string from bugsigDB output containing comma separated
+#' Metaphlan taxonomic names
+#'
+#' @return sig.list , a character list of containing the string after the last
+#'  "|" in each comma separated Metaphlan taxonomic name
+#'
+#' @export
+getSigList <- function(sig){
+  sig.list <- sub("^.+\\|", "", unlist(strsplit(sig ,",")))
+  return(sig.list)
+}
diff --git a/R/microbeEntries.R b/R/microbeEntries.R
new file mode 100644
index 0000000..384d9ba
--- /dev/null
+++ b/R/microbeEntries.R
@@ -0,0 +1,32 @@
+#' Microbe Entries
+#' A function that can be used to call of specific microbe signatures.
+#' @param query Name of the signature group. If query is passed "all" function will return all the signature groups
+#'
+#' @return The microbes within a desired signature group in the format "x__microbe name" with x indicating taxonomic level
+#' @export
+#'
+#' @examples microbeEntries("paa_up")
+microbeEntries <- function(query){
+
+  paa_up <- c("s__Clostridium sp. UNK-MGS-6", "s__Firmicutes bacterium CAG 41",
+              "s__Coprobacillus cateniformis", "s__Clostridia bacterium UC5-1-2G4",
+              "s__Streptococcus dysgalactiae", "s__Acidaminococcus sp. HPA0509",
+              "s__Roseburia sp.CAG-303", "s__Butyrivibrio_sp. AE2032",
+              "s__Coprobacillus sp. 29-1", "s__Coprobacillus sp. D6")
+  paa_down <- c("s__Alistipes sp. CAG-435", "s__Fusobacterium hwasookii",
+                "s__Leuconostoc sp. DORA-2", "s__Paenibacillus lentimorbus",
+                "s__Fusobacterium sp. oral taxon 370", "s__Alcanivorax hongdengensis",
+                "s__Arthrobacter sp. LS16", "s__Bacillus sp. 5B6", "s__Bacillus velezensis",
+                "s__Fusobacterium sp. OBRC1")
+
+  mic_list <- list(paa_up, paa_down)
+
+  names(mic_list) <- c("paa_up", "paa_down")
+
+  if(query == "all"){
+    return(mic_list)
+  }
+
+  mics_queried <- mic_list[[query]]
+  return(mics_queried)
+}
diff --git a/README.md b/README.md
index 6b527ab..0799258 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,2 @@
 # microsig
-This package contains functions to calculate microbe signatures, particularly from bugsigdb inputs.
+This package contains functions to calculate microbe signature scores, particularly from bugsigdb inputs.
diff --git a/man/calcMicroSigScore.Rd b/man/calcMicroSigScore.Rd
new file mode 100644
index 0000000..cedfaed
--- /dev/null
+++ b/man/calcMicroSigScore.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/calcMicroSigScore.R
+\name{calcMicroSigScore}
+\alias{calcMicroSigScore}
+\title{Function to calculate microbe signature scores given a set of up and down
+regulated microbes and the relative abundances of microbe per sample}
+\usage{
+calcMicroSigScore(taxa, sig.up, sig.down)
+}
+\arguments{
+\item{taxa}{a data frame where columns are microbes and rows are samples, first
+column named 'sample'}
+
+\item{sig.up}{a character vector listing microbes in given signature that are
+up-regulated, empty if none}
+
+\item{sig.down}{a character vector listing microbes in given signature that are
+down-regulated, empty if none}
+}
+\value{
+a data frame with samples and corresponding microbe signature scores
+}
+\description{
+Function to calculate microbe signature scores given a set of up and down
+regulated microbes and the relative abundances of microbe per sample
+}
diff --git a/man/getSigList.Rd b/man/getSigList.Rd
new file mode 100644
index 0000000..fdedaa2
--- /dev/null
+++ b/man/getSigList.Rd
@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/getSigList.R
+\name{getSigList}
+\alias{getSigList}
+\title{Given a single cell value from bigsigDB output in the column 'MetaPhlAn.taxon.names',
+returns a list of the microbes}
+\usage{
+getSigList(sig)
+}
+\arguments{
+\item{sig}{character string from bugsigDB output containing comma separated
+Metaphlan taxonomic names}
+}
+\value{
+sig.list , a character list of containing the string after the last
+"|" in each comma separated Metaphlan taxonomic name
+}
+\description{
+Given a single cell value from bigsigDB output in the column 'MetaPhlAn.taxon.names',
+returns a list of the microbes
+}
diff --git a/man/microbeEntries.Rd b/man/microbeEntries.Rd
new file mode 100644
index 0000000..d7ff5bf
--- /dev/null
+++ b/man/microbeEntries.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/microbeEntries.R
+\name{microbeEntries}
+\alias{microbeEntries}
+\title{Microbe Entries
+A function that can be used to call of specific microbe signatures.}
+\usage{
+microbeEntries(query)
+}
+\arguments{
+\item{query}{Name of the signature group. If query is passed "all" function will return all the signature groups}
+}
+\value{
+The microbes within a desired signature group in the format "x__microbe name" with x indicating taxonomic level
+}
+\description{
+Microbe Entries
+A function that can be used to call of specific microbe signatures.
+}
+\examples{
+microbeEntries("paa_up")
+}
diff --git a/microsig.Rproj b/microsig.Rproj
new file mode 100644
index 0000000..e83436a
--- /dev/null
+++ b/microsig.Rproj
@@ -0,0 +1,16 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes