diff --git a/NAMESPACE b/NAMESPACE
index fe4c23d6..4c05dc94 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(BinaryDomainNetwork)
 export(GCA2Lineage)
-export(GenContextNetwork)
 export(IPG2Lineage)
 export(acc2FA)
 export(acc2Lineage)
@@ -29,14 +27,19 @@ export(convertAlignment2FA)
 export(convertAlignment2Trees)
 export(convertFA2Tree)
 export(countByColumn)
+export(createBinaryDomainNetwork)
+export(createDomainNetwork)
 export(createFA2Tree)
+export(createGenomicContextNetwork)
 export(createJobResultsURL)
 export(createJobStatusEmailMessage)
+export(createMSA_Kalign)
+export(createMSA_PDF)
 export(createRepresentativeAccNum)
+export(createUndirectedGenomicContextNetwork)
 export(createWordCloud2Element)
 export(createWordCloudElement)
 export(create_lineage_lookup)
-export(domain_network)
 export(downloadAssemblySummary)
 export(efetchIPG)
 export(extractAccNum)
@@ -44,9 +47,7 @@ export(filterByDomains)
 export(filterByFrequency)
 export(findParalogs)
 export(formatJobArgumentsHTML)
-export(gc_undirected_network)
 export(generateAllAlignments2FA)
-export(generate_msa)
 export(getAccNumFromFA)
 export(getTopAccByLinDomArch)
 export(get_proc_medians)
@@ -54,7 +55,6 @@ export(get_proc_weights)
 export(make_opts2procs)
 export(mapAcc2Name)
 export(map_advanced_opts2procs)
-export(msa_pdf)
 export(plotIPR2Viz)
 export(plotIPR2VizWeb)
 export(plotLineageDA)
diff --git a/man/BinaryDomainNetwork.Rd b/man/createBinaryDomainNetwork.Rd
similarity index 92%
rename from man/BinaryDomainNetwork.Rd
rename to man/createBinaryDomainNetwork.Rd
index bb7e2353..4f0bdc5a 100644
--- a/man/BinaryDomainNetwork.Rd
+++ b/man/createBinaryDomainNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_domarch.R
-\name{BinaryDomainNetwork}
-\alias{BinaryDomainNetwork}
+\name{createBinaryDomainNetwork}
+\alias{createBinaryDomainNetwork}
 \title{Domain Network}
 \usage{
-BinaryDomainNetwork(
+createBinaryDomainNetwork(
   prot,
   column = "DomArch",
   domains_of_interest,
@@ -42,6 +42,6 @@ A network of domains is returned based on shared domain architectures.
 }
 \examples{
 \dontrun{
-domain_network(pspa)
+createDomainNetwork(pspa)
 }
 }
diff --git a/man/domain_network.Rd b/man/createDomainNetwork.Rd
similarity index 90%
rename from man/domain_network.Rd
rename to man/createDomainNetwork.Rd
index 528e4924..1588af17 100644
--- a/man/domain_network.Rd
+++ b/man/createDomainNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_domarch.R
-\name{domain_network}
-\alias{domain_network}
+\name{createDomainNetwork}
+\alias{createDomainNetwork}
 \title{Domain Network}
 \usage{
-domain_network(
+createDomainNetwork(
   prot,
   column = "DomArch",
   domains_of_interest,
@@ -33,6 +33,6 @@ A network of domains is returned based on shared domain architectures.
 }
 \examples{
 \dontrun{
-domain_network(pspa)
+createDomainNetwork(pspa)
 }
 }
diff --git a/man/GenContextNetwork.Rd b/man/createGenomicContextNetwork.Rd
similarity index 91%
rename from man/GenContextNetwork.Rd
rename to man/createGenomicContextNetwork.Rd
index 2eeebbc5..ac6deb84 100644
--- a/man/GenContextNetwork.Rd
+++ b/man/createGenomicContextNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_gencontext.R
-\name{GenContextNetwork}
-\alias{GenContextNetwork}
+\name{createGenomicContextNetwork}
+\alias{createGenomicContextNetwork}
 \title{Genomic Context Directed Network}
 \usage{
-GenContextNetwork(
+createGenomicContextNetwork(
   prot,
   domains_of_interest,
   column = "GenContext",
diff --git a/man/generate_msa.Rd b/man/createMSA_Kalign.Rd
similarity index 70%
rename from man/generate_msa.Rd
rename to man/createMSA_Kalign.Rd
index a68eb8b4..946f04ae 100644
--- a/man/generate_msa.Rd
+++ b/man/createMSA_Kalign.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/msa.R
-\name{generate_msa}
-\alias{generate_msa}
+\name{createMSA_Kalign}
+\alias{createMSA_Kalign}
 \title{Function to generate MSA using kalign}
 \usage{
-generate_msa(fa_file = "", outfile = "")
+createMSA_Kalign(fa_file = "", outfile = "")
 }
 \arguments{
 \item{outfile}{}
diff --git a/man/msa_pdf.Rd b/man/createMSA_PDF.Rd
similarity index 77%
rename from man/msa_pdf.Rd
rename to man/createMSA_PDF.Rd
index 4d5fed17..7cd7516a 100644
--- a/man/msa_pdf.Rd
+++ b/man/createMSA_PDF.Rd
@@ -1,10 +1,15 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/msa.R
-\name{msa_pdf}
-\alias{msa_pdf}
+\name{createMSA_PDF}
+\alias{createMSA_PDF}
 \title{Multiple Sequence Alignment}
 \usage{
-msa_pdf(fasta_path, out_path = NULL, lowerbound = NULL, upperbound = NULL)
+createMSA_PDF(
+  fasta_path,
+  out_path = NULL,
+  lowerbound = NULL,
+  upperbound = NULL
+)
 }
 \arguments{
 \item{fasta_path}{Character. The path location of the fasta file to be read.}
@@ -21,11 +26,11 @@ Default is NULL. If value is NULL, the entire multiple sequence alignment is pri
 \description{
 Generates a multiple sequence alignment from a fasta file
 
-msa_pdf is a function that reads a fasta file and generates a multiple sequence alignment as
+createMSA_PDF is a function that reads a fasta file and generates a multiple sequence alignment as
 a pdf
 }
 \examples{
 \dontrun{
-msa_pdf()
+createMSA_PDF()
 }
 }
diff --git a/man/gc_undirected_network.Rd b/man/createUndirectedGenomicContextNetwork.Rd
similarity index 90%
rename from man/gc_undirected_network.Rd
rename to man/createUndirectedGenomicContextNetwork.Rd
index 28cf1abb..d61c23df 100644
--- a/man/gc_undirected_network.Rd
+++ b/man/createUndirectedGenomicContextNetwork.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/networks_gencontext.R
-\name{gc_undirected_network}
-\alias{gc_undirected_network}
+\name{createUndirectedGenomicContextNetwork}
+\alias{createUndirectedGenomicContextNetwork}
 \title{Domain Network}
 \usage{
-gc_undirected_network(
+createUndirectedGenomicContextNetwork(
   prot,
   column = "GenContext",
   domains_of_interest,