{"id":274,"date":"2024-05-06T23:43:57","date_gmt":"2024-05-06T23:43:57","guid":{"rendered":"https:\/\/sites.wp.odu.edu\/awolter\/?post_type=portfolio&#038;p=274"},"modified":"2024-05-06T23:43:57","modified_gmt":"2024-05-06T23:43:57","slug":"bioconductor-functions","status":"publish","type":"portfolio","link":"https:\/\/sites.wp.odu.edu\/awolter\/portfolio\/bioconductor-functions\/","title":{"rendered":"Bioconductor functions"},"content":{"rendered":" <p><strong>Installing<\/strong><\/p>    <hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>    <p>BiocManager::install(&#8220;Biostrings&#8221;)<\/p>    <p>Libraries<\/p>    <p>library(rentrez)<\/p>    <p>library(genbankr) <\/p>    <p>library(DECIPHER) <\/p>    <p>library(ggtree) <\/p>    <hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>    <p><\/p>    <p><strong>Biostrings<\/strong><\/p>    <p>unlist() # coallates multiple elements into a single sequence. <\/p>    <p>Length() <\/p>    <p>width() # number of characters per sequence, used in sets. <\/p>    <p>complement() # produces a complement strand. <\/p>    <p>rev() #changes sequence order from top to bottom.. <\/p>    <p>reverse(). # changes order from left to right 2<\/p>    <p>reverseComplement() # reverses the complement of the sequence. <\/p>    <p>subseq() # subset 1 or more sequences from an existing sequence. <\/p>    <p><\/p>    <p><strong>SHORT Reads<\/strong><\/p>    <hr class=\"wp-block-separator has-alpha-channel-opacity\" \/>    <p>readFasta() <\/p>    <p>readFastq() <\/p>    <p>writeFastq() <\/p>    <p>set.seed() <\/p>    <p>alphabetByCycle() # letter frequencies per cycle. <\/p>    <p>sread() # extract sequence from short read object <\/p>    <p>class() # check class of sample. <\/p>    <p>quality() # check quality of sequence, given in encoding values. <\/p>    <p>PhredQuality() # transform encoding values of quality. <\/p>    <p>yeild() # extracts information from stored file. <\/p>    <p>methods(class = &#8220;ShortRead&#8221;) # methods accessors for fasta. <\/p>    <p>methods(class = &#8220;ShortReadQ&#8221;) # methods accessors for fastq. <\/p>    <p>polynFilter() #selects reads that contain less than the given number of duplicate nucleotides. <\/p> ","protected":false},"excerpt":{"rendered":"<p>Installing BiocManager::install(&#8220;Biostrings&#8221;) Libraries library(rentrez) library(genbankr) library(DECIPHER) library(ggtree) Biostrings unlist() # coallates multiple elements into a single sequence. Length() width() # number of characters per sequence, used in sets. complement() # produces a complement strand. rev() #changes sequence order from top to bottom.. reverse(). # changes order from left to right 2 reverseComplement() # reverses the [&hellip;]<\/p>\n","protected":false},"author":28160,"featured_media":0,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"wds_primary_portfolio-type":0},"portfolio-type":[],"_links":{"self":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/portfolio\/274"}],"collection":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/portfolio"}],"about":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/types\/portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/users\/28160"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/comments?post=274"}],"wp:attachment":[{"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/media?parent=274"}],"wp:term":[{"taxonomy":"portfolio-type","embeddable":true,"href":"https:\/\/sites.wp.odu.edu\/awolter\/wp-json\/wp\/v2\/portfolio-type?post=274"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}