From 97577c32448620d6349a60ed11e9edae5b242f49 Mon Sep 17 00:00:00 2001 From: Fawaz Dabbaghieh Date: Mon, 19 Mar 2018 23:32:20 +0100 Subject: [PATCH] help page as markdown --- gene_ids/protein_coding_HAVANA_genes_ids.txt | 19561 +++++++++++++++++ help/example.jpg | Bin 0 -> 44444 bytes help/list_experiments_tab.md | 157 + help/score_matrix_tab.md | 157 + 4 files changed, 19875 insertions(+) create mode 100644 gene_ids/protein_coding_HAVANA_genes_ids.txt create mode 100644 help/example.jpg create mode 100644 help/list_experiments_tab.md create mode 100644 help/score_matrix_tab.md diff --git a/gene_ids/protein_coding_HAVANA_genes_ids.txt b/gene_ids/protein_coding_HAVANA_genes_ids.txt new file mode 100644 index 0000000..00a3a77 --- /dev/null +++ b/gene_ids/protein_coding_HAVANA_genes_ids.txt @@ -0,0 +1,19561 @@ +ENSG00000186092.4 +ENSG00000278566.1 +ENSG00000273547.1 +ENSG00000187634.10 +ENSG00000188976.10 +ENSG00000187961.13 +ENSG00000187583.10 +ENSG00000187642.9 +ENSG00000188290.10 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Itemized lists +look like: + + * this one + * that one + * the other one + +Note that --- not considering the asterisk --- the actual text +content starts at 4-columns in. + +> Block quotes are +> written like so. +> +> They can span multiple paragraphs, +> if you like. + +Use 3 dashes for an em-dash. Use 2 dashes for ranges (ex., "it's all +in chapters 12--14"). Three dots ... will be converted to an ellipsis. +Unicode is supported. ☺ + + + +An h2 header +------------ + +Here's a numbered list: + + 1. first item + 2. second item + 3. third item + +Note again how the actual text starts at 4 columns in (4 characters +from the left side). Here's a code sample: + + # Let me re-iterate ... + for i in 1 .. 10 { do-something(i) } + +As you probably guessed, indented 4 spaces. By the way, instead of +indenting the block, you can use delimited blocks, if you like: + +~~~ +define foobar() { + print "Welcome to flavor country!"; +} +~~~ + +(which makes copying & pasting easier). You can optionally mark the +delimited block for Pandoc to syntax highlight it: + +~~~python +import time +# Quick, count to ten! +for i in range(10): + # (but not *too* quick) + time.sleep(0.5) + print i +~~~ + + + +### An h3 header ### + +Now a nested list: + + 1. First, get these ingredients: + + * carrots + * celery + * lentils + + 2. Boil some water. + + 3. Dump everything in the pot and follow + this algorithm: + + find wooden spoon + uncover pot + stir + cover pot + balance wooden spoon precariously on pot handle + wait 10 minutes + goto first step (or shut off burner when done) + + Do not bump wooden spoon or it will fall. + +Notice again how text always lines up on 4-space indents (including +that last line which continues item 3 above). + +Here's a link to [a website](http://foo.bar), to a [local +doc](local-doc.html), and to a [section heading in the current +doc](#an-h2-header). Here's a footnote [^1]. + +[^1]: Footnote text goes here. + +Tables can look like this: + +size material color +---- ------------ ------------ +9 leather brown +10 hemp canvas natural +11 glass transparent + +Table: Shoes, their sizes, and what they're made of + +(The above is the caption for the table.) Pandoc also supports +multi-line tables: + +-------- ----------------------- +keyword text +-------- ----------------------- +red Sunsets, apples, and + other red or reddish + things. + +green Leaves, grass, frogs + and other things it's + not easy being. +-------- ----------------------- + +A horizontal rule follows. + +*** + +Here's a definition list: + +apples + : Good for making applesauce. +oranges + : Citrus! +tomatoes + : There's no "e" in tomatoe. + +Again, text is indented 4 spaces. (Put a blank line between each +term/definition pair to spread things out more.) + +Here's a "line block": + +| Line one +| Line too +| Line tree + +and images can be specified like so: + +![example image](example.jpg "An exemplary image") + +Inline math equations go in like so: $\omega = d\phi / dt$. Display +math should get its own line and be put in in double-dollarsigns: + +$$I = \int \rho R^{2} dV$$ + +And note that you can backslash-escape any punctuation characters +which you wish to be displayed literally, ex.: \`foo\`, \*bar\*, etc. \ No newline at end of file diff --git a/help/score_matrix_tab.md b/help/score_matrix_tab.md new file mode 100644 index 0000000..e8a43fc --- /dev/null +++ b/help/score_matrix_tab.md @@ -0,0 +1,157 @@ +Score Matrix Tab Help Page +============ + +Paragraphs are separated by a blank line. + +2nd paragraph. *Italic*, **bold**, and `monospace`. Itemized lists +look like: + + * this one + * that one + * the other one + +Note that --- not considering the asterisk --- the actual text +content starts at 4-columns in. + +> Block quotes are +> written like so. +> +> They can span multiple paragraphs, +> if you like. + +Use 3 dashes for an em-dash. Use 2 dashes for ranges (ex., "it's all +in chapters 12--14"). Three dots ... will be converted to an ellipsis. +Unicode is supported. ☺ + + + +An h2 header +------------ + +Here's a numbered list: + + 1. first item + 2. second item + 3. third item + +Note again how the actual text starts at 4 columns in (4 characters +from the left side). Here's a code sample: + + # Let me re-iterate ... + for i in 1 .. 10 { do-something(i) } + +As you probably guessed, indented 4 spaces. By the way, instead of +indenting the block, you can use delimited blocks, if you like: + +~~~ +define foobar() { + print "Welcome to flavor country!"; +} +~~~ + +(which makes copying & pasting easier). You can optionally mark the +delimited block for Pandoc to syntax highlight it: + +~~~python +import time +# Quick, count to ten! +for i in range(10): + # (but not *too* quick) + time.sleep(0.5) + print i +~~~ + + + +### An h3 header ### + +Now a nested list: + + 1. First, get these ingredients: + + * carrots + * celery + * lentils + + 2. Boil some water. + + 3. Dump everything in the pot and follow + this algorithm: + + find wooden spoon + uncover pot + stir + cover pot + balance wooden spoon precariously on pot handle + wait 10 minutes + goto first step (or shut off burner when done) + + Do not bump wooden spoon or it will fall. + +Notice again how text always lines up on 4-space indents (including +that last line which continues item 3 above). + +Here's a link to [a website](http://foo.bar), to a [local +doc](local-doc.html), and to a [section heading in the current +doc](#an-h2-header). Here's a footnote [^1]. + +[^1]: Footnote text goes here. + +Tables can look like this: + +size material color +---- ------------ ------------ +9 leather brown +10 hemp canvas natural +11 glass transparent + +Table: Shoes, their sizes, and what they're made of + +(The above is the caption for the table.) Pandoc also supports +multi-line tables: + +-------- ----------------------- +keyword text +-------- ----------------------- +red Sunsets, apples, and + other red or reddish + things. + +green Leaves, grass, frogs + and other things it's + not easy being. +-------- ----------------------- + +A horizontal rule follows. + +*** + +Here's a definition list: + +apples + : Good for making applesauce. +oranges + : Citrus! +tomatoes + : There's no "e" in tomatoe. + +Again, text is indented 4 spaces. (Put a blank line between each +term/definition pair to spread things out more.) + +Here's a "line block": + +| Line one +| Line too +| Line tree + +and images can be specified like so: + +![example image](example.jpg "An exemplary image") + +Inline math equations go in like so: $\omega = d\phi / dt$. Display +math should get its own line and be put in in double-dollarsigns: + +$$I = \int \rho R^{2} dV$$ + +And note that you can backslash-escape any punctuation characters +which you wish to be displayed literally, ex.: \`foo\`, \*bar\*, etc. \ No newline at end of file