markdown source builds

Auto-generated via {sandpaper}
Source  : f711a4a
Branch  : main
Author  : Kevin Rue-Albrecht <kevinrue67@gmail.com>
Time    : 2024-08-01 14:12:29 +0000
Message : fix download of imput data (#91)

01-setup.md

@@ -63,15 +63,15 @@ download.file(
 )
 download.file(
   url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/counts.csv",
-  destfile = "data/actb_orfs.fasta"
+  destfile = "data/counts.csv"
 )
 download.file(
   url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/gene_metadata.csv",
-  destfile = "data/actb_orfs.fasta"
+  destfile = "data/gene_metadata.csv"
 )
 download.file(
   url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/sample_metadata.csv",
-  destfile = "data/actb_orfs.fasta"
+  destfile = "data/sample_metadata.csv"
 )
 ```
 

data/actb_orfs.fasta

@@ -1,5 +1,66 @@
-id,condition,batch
-sample_1,A,1
-sample_2,A,2
-sample_3,B,1
-sample_4,B,2
+>gi|1519311456|ref|NM_001101.5|:c224-3 ORF12 CDS
+ATGCCCACCATCACGCCCTGGTGCCTGGGGCGCCCCACGATGGAGGGGAAGACGGCCCGGGGGGCATCGT
+CGCCCGCGAAGCCGGCCTTGCACATGCCGGAGCCGTTGTCGACGACGAGCGCGGCGATATCATCATCCAT
+GGTGAGCTGGCGGCGGGTGTGGACGGGCGGCGGATCGGCAAAGGCGAGGCTCTGTGCTCGCGGGGCGGAC
+GCGGTCTCGGCG
+>gi|1519311456|ref|NM_001101.5|:85-1212 ORF1 CDS
+ATGGATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGGCATGTGCAAGGCCGGCTTCGCGGGCG
+ACGATGCCCCCCGGGCCGTCTTCCCCTCCATCGTGGGGCGCCCCAGGCACCAGGGCGTGATGGTGGGCAT
+GGGTCAGAAGGATTCCTATGTGGGCGACGAGGCCCAGAGCAAGAGAGGCATCCTCACCCTGAAGTACCCC
+ATCGAGCACGGCATCGTCACCAACTGGGACGACATGGAGAAAATCTGGCACCACACCTTCTACAATGAGC
+TGCGTGTGGCTCCCGAGGAGCACCCCGTGCTGCTGACCGAGGCCCCCCTGAACCCCAAGGCCAACCGCGA
+GAAGATGACCCAGATCATGTTTGAGACCTTCAACACCCCAGCCATGTACGTTGCTATCCAGGCTGTGCTA
+TCCCTGTACGCCTCTGGCCGTACCACTGGCATCGTGATGGACTCCGGTGACGGGGTCACCCACACTGTGC
+CCATCTACGAGGGGTATGCCCTCCCCCATGCCATCCTGCGTCTGGACCTGGCTGGCCGGGACCTGACTGA
+CTACCTCATGAAGATCCTCACCGAGCGCGGCTACAGCTTCACCACCACGGCCGAGCGGGAAATCGTGCGT
+GACATTAAGGAGAAGCTGTGCTACGTCGCCCTGGACTTCGAGCAAGAGATGGCCACGGCTGCTTCCAGCT
+CCTCCCTGGAGAAGAGCTACGAGCTGCCTGACGGCCAGGTCATCACCATTGGCAATGAGCGGTTCCGCTG
+CCCTGAGGCACTCTTCCAGCCTTCCTTCCTGGGCATGGAGTCCTGTGGCATCCACGAAACTACCTTCAAC
+TCCATCATGAAGTGTGACGTGGACATCCGCAAAGACCTGTACGCCAACACAGTGCTGTCTGGCGGCACCA
+CCATGTACCCTGGCATTGCCGACAGGATGCAGAAGGAGATCACTGCCCTGGCACCCAGCACAATGAAGAT
+CAAGATCATTGCTCCTCCTGAGCGCAAGTACTCCGTGTGGATCGGCGGCTCCATCCTGGCCTCGCTGTCC
+ACCTTCCAGCAGATGTGGATCAGCAAGCAGGAGTATGACGAGTCCGGCCCCTCCATCGTCCACCGCAAAT
+GCTTCTAG
+>gi|1519311456|ref|NM_001101.5|:89-214 ORF4 CDS
+ATGATGATATCGCCGCGCTCGTCGTCGACAACGGCTCCGGCATGTGCAAGGCCGGCTTCGCGGGCGACGA
+TGCCCCCCGGGCCGTCTTCCCCTCCATCGTGGGGCGCCCCAGGCACCAGGGCGTGA
+>gi|1519311456|ref|NM_001101.5|:c329-240 ORF11 CDS
+ATGTCGTCCCAGTTGGTGACGATGCCGTGCTCGATGGGGTACTTCAGGGTGAGGATGCCTCTCTTGCTCT
+GGGCCTCGTCGCCCACATAG
+>gi|1519311456|ref|NM_001101.5|:c578-354 ORF10 CDS
+ATGGGCACAGTGTGGGTGACCCCGTCACCGGAGTCCATCACGATGCCAGTGGTACGGCCAGAGGCGTACA
+GGGATAGCACAGCCTGGATAGCAACGTACATGGCTGGGGTGTTGAAGGTCTCAAACATGATCTGGGTCAT
+CTTCTCGCGGTTGGCCTTGGGGTTCAGGGGGGCCTCGGTCAGCAGCACGGGGTGCTCCTCGGGAGCCACA
+CGCAGCTCATTGTAG
+>gi|1519311456|ref|NM_001101.5|:c603-502 ORF8 CDS
+ATGGGGGAGGGCATACCCCTCGTAGATGGGCACAGTGTGGGTGACCCCGTCACCGGAGTCCATCACGATG
+CCAGTGGTACGGCCAGAGGCGTACAGGGATAG
+>gi|1519311456|ref|NM_001101.5|:c1190-801 ORF9 CDS
+ATGGAGGGGCCGGACTCGTCATACTCCTGCTTGCTGATCCACATCTGCTGGAAGGTGGACAGCGAGGCCA
+GGATGGAGCCGCCGATCCACACGGAGTACTTGCGCTCAGGAGGAGCAATGATCTTGATCTTCATTGTGCT
+GGGTGCCAGGGCAGTGATCTCCTTCTGCATCCTGTCGGCAATGCCAGGGTACATGGTGGTGCCGCCAGAC
+AGCACTGTGTTGGCGTACAGGTCTTTGCGGATGTCCACGTCACACTTCATGATGGAGTTGAAGGTAGTTT
+CGTGGATGCCACAGGACTCCATGCCCAGGAAGGAAGGCTGGAAGAGTGCCTCAGGGCAGCGGAACCGCTC
+ATTGCCAATGGTGATGACCTGGCCGTCAGGCAGCTCGTAG
+>gi|1519311456|ref|NM_001101.5|:839-934 ORF5 CDS
+ATGAGCGGTTCCGCTGCCCTGAGGCACTCTTCCAGCCTTCCTTCCTGGGCATGGAGTCCTGTGGCATCCA
+CGAAACTACCTTCAACTCCATCATGA
+>gi|1519311456|ref|NM_001101.5|:1277-1618 ORF6 CDS
+ATGAGATTGGCATGGCTTTATTTGTTTTTTTTGTTTTGTTTTGGTTTTTTTTTTTTTTTTGGCTTGACTC
+AGGATTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTTCACAAT
+GTGGCCGAGGACTTTGATTGCACATTGTTGTTTTTTTAATAGTCATTCCAAATATGAGATGCGTTGTTAC
+AGGAAGTCCCTTGCCATCCTAAAAGCCACCCCACTTCTCTCTAAGGAGAATGGCCCAGTCCTCTCCCAAG
+TCCACACAGGGGAGGTGATAGCATTGCTTTCGTGTAAATTATGTAATGCAAAATTTTTTTAA
+>gi|1519311456|ref|NM_001101.5|:1288-1455 ORF2 CDS
+ATGGCTTTATTTGTTTTTTTTGTTTTGTTTTGGTTTTTTTTTTTTTTTTGGCTTGACTCAGGATTTAAAA
+ACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTTCACAATGTGGCCGAGGA
+CTTTGATTGCACATTGTTGTTTTTTTAA
+>gi|1519311456|ref|NM_001101.5|:c1462-1352 ORF13 CDS
+ATGACTATTAAAAAAACAACAATGTGCAATCAAAGTCCTCGGCCACATTGTGAACTTTGGGGGATGCTCG
+CTCCAACCGACTGCTGTCACCTTCACCGTTCCAGTTTTTAA
+>gi|1519311456|ref|NM_001101.5|:1602-1706 ORF7 CDS
+ATGCAAAATTTTTTTAATCTTCGCCTTAATACTTTTTTATTTTGTTTTATTTTGAATGATGAGCCTTCGT
+GCCCCCCCTTCCCCCTTTTTTGTCCCCCAACTTGA
+>gi|1519311456|ref|NM_001101.5|:1657-1791 ORF3 CDS
+ATGATGAGCCTTCGTGCCCCCCCTTCCCCCTTTTTTGTCCCCCAACTTGAGATGTATGAAGGCTTTTGGT
+CTCCCTGGGAGTGGGTGGAGGCAGCCAGGGCTTACCTGTACACTGACTTGAGACCAGTTGAATAA

data/counts.csv

@@ -0,0 +1,26 @@
+feature,sample_1,sample_2,sample_3,sample_4
+gene_1,109,84,91,105
+gene_2,111,97,98,108
+gene_3,89,121,105,99
+gene_4,105,109,122,101
+gene_5,82,97,112,83
+gene_6,89,96,90,116
+gene_7,121,95,88,106
+gene_8,101,101,86,103
+gene_9,91,119,89,87
+gene_10,81,111,81,118
+gene_11,93,118,93,99
+gene_12,103,111,116,103
+gene_13,89,126,103,100
+gene_14,101,107,111,79
+gene_15,96,91,103,108
+gene_16,110,102,128,103
+gene_17,95,106,118,100
+gene_18,99,115,114,102
+gene_19,114,105,94,118
+gene_20,110,88,99,102
+gene_21,116,95,94,105
+gene_22,114,96,107,91
+gene_23,97,120,93,90
+gene_24,91,84,118,97
+gene_25,99,106,97,110

data/gene_metadata.csv

@@ -0,0 +1,26 @@
+id,chromosome
+gene_1,4
+gene_2,4
+gene_3,5
+gene_4,4
+gene_5,5
+gene_6,1
+gene_7,2
+gene_8,1
+gene_9,3
+gene_10,1
+gene_11,1
+gene_12,5
+gene_13,5
+gene_14,1
+gene_15,3
+gene_16,4
+gene_17,2
+gene_18,5
+gene_19,1
+gene_20,3
+gene_21,5
+gene_22,5
+gene_23,1
+gene_24,4
+gene_25,5

data/sample_metadata.csv

@@ -0,0 +1,5 @@
+id,condition,batch
+sample_1,A,1
+sample_2,A,2
+sample_3,B,1
+sample_4,B,2

download_data.R

@@ -14,13 +14,13 @@ download.file(
 )
 download.file(
   url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/counts.csv",
-  destfile = "data/actb_orfs.fasta"
+  destfile = "data/counts.csv"
 )
 download.file(
   url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/gene_metadata.csv",
-  destfile = "data/actb_orfs.fasta"
+  destfile = "data/gene_metadata.csv"
 )
 download.file(
   url = "https://raw.githubusercontent.com/Bioconductor/bioconductor-teaching/devel/data/SummarizedExperiment/sample_metadata.csv",
-  destfile = "data/actb_orfs.fasta"
+  destfile = "data/sample_metadata.csv"
 )

md5sum.txt

@@ -3,7 +3,7 @@
 "LICENSE.md" "afaf427b4223952624dcb6d8ded53ec0" "site/built/LICENSE.md" "2024-07-31"
 "config.yaml" "865bc02946e1c148f8b2374313178780" "site/built/config.yaml" "2024-08-01"
 "index.md" "6cf23d25cc71edcff0cdd1f6d60039da" "site/built/index.md" "2024-07-31"
-"episodes/01-setup.Rmd" "54ecc365df019150e95e6aaf67cc7859" "site/built/01-setup.md" "2024-08-01"
+"episodes/01-setup.Rmd" "19f06a730c60c7a4a87c26ec49f3c092" "site/built/01-setup.md" "2024-08-01"
 "episodes/02-introduction-to-bioconductor.Rmd" "95db83520fedb68fb63fc660fb583ff5" "site/built/02-introduction-to-bioconductor.md" "2024-07-31"
 "episodes/03-installing-bioconductor.Rmd" "54bbda53c9e93e35c098c510ebdbd12a" "site/built/03-installing-bioconductor.md" "2024-07-31"
 "episodes/04-getting-help.Rmd" "ef95b83e2cf1db86786c9b8ff971684b" "site/built/04-getting-help.md" "2024-07-31"