diff --git a/docs/Intro_to_R_data_analysis_part_1.html b/docs/Intro_to_R_data_analysis_part_1.html index 617a1ff..2cfd342 100644 --- a/docs/Intro_to_R_data_analysis_part_1.html +++ b/docs/Intro_to_R_data_analysis_part_1.html @@ -2923,7 +2923,7 @@ types/structures (ex. nested lists)

10 min break

-
+
10:00
diff --git a/docs/Intro_to_Unix_Part_1.html b/docs/Intro_to_Unix_Part_1.html index 8c45585..4703e7f 100644 --- a/docs/Intro_to_Unix_Part_1.html +++ b/docs/Intro_to_Unix_Part_1.html @@ -4,7 +4,7 @@ - Introduction to Unix Command-line - Part 1 + Introduction to Unix Command-line @@ -1878,9 +1878,10 @@ document.addEventListener('DOMContentLoaded', function(e) {
-

Introduction to Unix Command-line - Part 1

+

Introduction to Unix Command-line

+

Part 1

Natalie Elphick

-

March 11th 2024

+

February 10th 2025

@@ -1894,8 +1895,8 @@ document.addEventListener('DOMContentLoaded', function(e) {

Natalie Elphick
Bioinformatician I


-

Ayushi Agrawal (TA)
-Bioinformatician III

+

Reuben Thomas
+Associate Core Director

@@ -1956,9 +1957,9 @@ each one: 
mkdir unix_workshop
cd unix_workshop
-
curl -L -o unix_workshop_2024.tar.gz 'https://www.dropbox.com/scl/fi/o8msrl3a1k986jvjll4mv/unix_workshop_2024.tar.gz?rlkey=m7jfkvpz0iq12zdzphq7013l5&dl=0'
-
tar -xzf unix_workshop_2024.tar.gz
-
cd unix_workshop_2024
+
curl -L -o unix_workshop.tar.gz 'https://www.dropbox.com/scl/fi/tdzpoivf7mienlenunqhf/unix_workshop.tar.gz?rlkey=6bfxnqgc5n4lgc9mc80ld75z4&dl=0'
+
tar -xzf unix_workshop.tar.gz
+
cd unix_workshop

The shell

@@ -2040,7 +2041,7 @@ STANDARDS The echo utility conforms to IEEE Std 1003.1-2001 (“POSIX.1”) as amended by Cor. 1-2002. -macOS 14.1 April 12, 2003 macOS 14.1 +macOS 14.4 April 12, 2003 macOS 14.4

Manual pages

@@ -2257,7 +2258,7 @@ SEE ALSO intro(3), intro(3lua), intro(4), intro(5), man.conf(5), intro(6), intro(7), mdoc(7), intro(8), intro(9) -macOS 14.1 January 9, 2021 macOS 14.1 +macOS 14.4 January 9, 2021 macOS 14.4

echo: print a string or value of a variable

@@ -2293,7 +2294,7 @@ terminal

The File System

-

Unix File system

+

Unix File system

Paths

@@ -2318,7 +2319,7 @@ terminal
What is the absolute path to file2.txt?
-

Unix File system

+

Unix File system

@@ -2326,12 +2327,12 @@ What is the absolute path to file2.txt? What is the realative path to file1.txt if the working directory is /home/user ?
-

Unix File system

+

Unix File system

pwd: print working directory

pwd
-
/Users/your_username/unix_workshop_2024
+
/Users/your_username/unix_workshop
ls -lah part_1
total 8
-drwx---rw-@ 4 nelphick  staff   128B Mar 12 09:18 .
-drwxr-xr-x@ 5 nelphick  staff   160B Mar 12 09:27 ..
+drwx---rw-@ 4 nelphick  staff   128B Feb 10 11:16 .
+drwxr-xr-x@ 5 nelphick  staff   160B Feb 10 11:16 ..
 -rw-r--r--@ 1 nelphick  staff     0B Apr 11  2023 .hidden_file.txt
 -rw-r--r--@ 1 nelphick  staff    60B Apr 12  2023 list_numbers.tsv

cd: move to a directory

-
cd unix_workshop_2024/part_1
+
cd unix_workshop/part_1
 ls -l

 
total 8
 -rw-r--r--@ 1 nelphick  staff  60 Apr 12  2023 list_numbers.tsv

 
cd ..
 ls -l

 
total 0
-drwx---rw-@ 4 nelphick  staff  128 Mar 12 09:18 part_1
-drwxr-xr-x@ 3 nelphick  staff   96 Mar 12 09:27 part_2

+drwx---rw-@ 4 nelphick  staff  128 Feb 10 11:16 part_1
+drwxr-xr-x@ 3 nelphick  staff   96 Feb 10 11:16 part_2
@@ -2375,7 +2376,7 @@ drwxr-xr-x@ 3 nelphick staff 96 Mar 12 09:27 part_2

File Permissions

-

File Permissions

+

File Permissions

File Permissions

-

File Permissions

+

File Permissions

Upcoming Data Science Training Program Workshops

-

Introduction -to Pathway Analysis
-April 2, 2024 1:00-4:00pm PDT

-

Statistics -of Enrichment Analysis Methods
-April 11-April 12, 2024 1:00-3:00pm PDT

-

Working on -Wynton
-April 15, 2024 1:00-4:00pm PDT

-

Introduction -to Linear Mixed Effects Models
-April 25-April 26, 2024 1:00-3:00pm PDT

+

Introduction +to RNA-Seq Analysis
+February 13-February 14, 2025 1:00-4:00pm PST

+

Intermediate +RNA-Seq Analysis Using R
+February 20, 2025 9:00am-12:00pm PST

+

Introduction +to Statistics, Experimental Design and Hypothesis Testing
+February 24-February 25, 2025 1:00-3:00pm PST

Complete Schedule

diff --git a/docs/Intro_to_Unix_Part_2.html b/docs/Intro_to_Unix_Part_2.html index 4adadad..272ca7a 100644 --- a/docs/Intro_to_Unix_Part_2.html +++ b/docs/Intro_to_Unix_Part_2.html @@ -4,7 +4,7 @@ - Introduction to Unix Command-line - Part 2 + Introduction to Unix Command-line @@ -1878,9 +1878,10 @@ document.addEventListener('DOMContentLoaded', function(e) {
-

Introduction to Unix Command-line - Part 2

+

Introduction to Unix Command-line

+

Part 2

Natalie Elphick

-

March 12th 2024

+

February 11th 2025

@@ -1892,7 +1893,7 @@ document.addEventListener('DOMContentLoaded', function(e) {

Introductions

Natalie Elphick
-Bioinformatician I

+Bioinformatician II


Yihang Xin (TA)
Software Engineer III

@@ -1903,11 +1904,11 @@ Software Engineer III

Run the following commands if you did not attend part 1:

mkdir unix_workshop
cd unix_workshop
-
curl -L -o unix_workshop_2024.tar.gz 'https://www.dropbox.com/scl/fi/o8msrl3a1k986jvjll4mv/unix_workshop_2024.tar.gz?rlkey=m7jfkvpz0iq12zdzphq7013l5&dl=0'
+
curl -L -o unix_workshop.tar.gz 'https://www.dropbox.com/scl/fi/tdzpoivf7mienlenunqhf/unix_workshop.tar.gz?rlkey=6bfxnqgc5n4lgc9mc80ld75z4&dl=0'
 

-
tar -xzf unix_workshop_2024.tar.gz

-
cd unix_workshop_2024

-
curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.111.refseq.tsv.gz

+
tar -xzf unix_workshop.tar.gz

+
cd unix_workshop

+
curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.113.refseq.tsv.gz
@@ -1937,7 +1938,7 @@ du -h part_2/homo_sapiens.refseq.tsv 
gzip part_2/homo_sapiens.refseq.tsv
 du -h part_2/homo_sapiens.refseq.tsv.gz
-
3.2M    part_2/homo_sapiens.refseq.tsv.gz
+
3.3M    part_2/homo_sapiens.refseq.tsv.gz
  • Compressing it makes it a 10th of the size
@@ -1962,9 +1963,9 @@ compressed archive files 
tar -czf part_1.tar.gz part_1
 ls -l
total 8
-drwx---rw-@ 4 nelphick  staff  128 Mar 12 09:36 part_1
--rw-r--r--  1 nelphick  staff  803 Mar 12 12:52 part_1.tar.gz
-drwxr-xr-x@ 4 nelphick  staff  128 Mar 12 12:52 part_2
+drwx---rw-@ 4 nelphick staff 128 Feb 10 11:16 part_1 +-rw-r--r-- 1 nelphick staff 801 Feb 10 11:16 part_1.tar.gz +drwxr-xr-x@ 4 nelphick staff 128 Feb 10 11:16 part_2
  • -c: create a new archive
  • -f: specify the name of the archive file
    • @@ -1992,7 +1993,6 @@ can use gunzip -c 
gunzip -c part_2/homo_sapiens.refseq.tsv.gz | head
gene_stable_id  transcript_stable_id    protein_stable_id   xref    db_name info_type   source_identity xref_identity   linkage_type
-ENSG00000228037 ENST00000424215 -   NR_121638   RefSeq_ncRNA    DIRECT  -   -   -
 ENSG00000142611 ENST00000378391 ENSP00000367643 NP_955533   RefSeq_peptide  DIRECT  100 100 -
 ENSG00000142611 ENST00000378391 ENSP00000367643 NM_199454   RefSeq_mRNA DIRECT  99  62  -
 ENSG00000142611 ENST00000270722 ENSP00000270722 NP_071397   RefSeq_peptide  DIRECT  100 100 -
@@ -2000,7 +2000,8 @@ ENSG00000142611 ENST00000270722 ENSP00000270722 NM_022114   RefSeq_mRNA DIRECT
 ENSG00000157911 ENST00000288774 ENSP00000288774 NP_001361354    RefSeq_peptide  INFERRED_PAIR   -   -   -
 ENSG00000157911 ENST00000288774 ENSP00000288774 NP_001361355    RefSeq_peptide  INFERRED_PAIR   -   -   -
 ENSG00000157911 ENST00000288774 ENSP00000288774 NP_722540   RefSeq_peptide  DIRECT  100 100 -
-ENSG00000157911 ENST00000288774 ENSP00000288774 NM_001374425    RefSeq_mRNA DIRECT  99  100 -
+ENSG00000157911 ENST00000288774 ENSP00000288774 NM_001374425 RefSeq_mRNA DIRECT 99 100 - +ENSG00000157911 ENST00000288774 ENSP00000288774 NM_001374426 RefSeq_mRNA DIRECT 94 92 -
@@ -2110,13 +2111,13 @@ interpreter is
  • By default, files are not executable
    • ls -l part_2/example_script.sh
    -
    -rw-r--r--  1 nelphick  staff  287 Mar 12 12:52 part_2/example_script.sh
    +
    -rw-r--r--  1 nelphick  staff  287 Feb 10 11:16 part_2/example_script.sh
    • We can set the execute bit like this
    chmod u+x part_2/example_script.sh
 ls -l part_2/example_script.sh
    -
    -rwxr--r--  1 nelphick  staff  287 Mar 12 12:52 part_2/example_script.sh
    +
    -rwxr--r--  1 nelphick  staff  287 Feb 10 11:16 part_2/example_script.sh

    Example

    @@ -2136,7 +2137,7 @@ echo "There are $u_genes unique genes in $1"

    Let’s run it

    ./part_2/example_script.sh part_2/homo_sapiens.refseq.tsv.gz
    Counting the genes in part_2/homo_sapiens.refseq.tsv.gz
-There are    33338 unique genes in part_2/homo_sapiens.refseq.tsv.gz
    +There are 36353 unique genes in part_2/homo_sapiens.refseq.tsv.gz

    Loops

    @@ -2270,7 +2271,7 @@ files awk -F '\t' '$5 == "RefSeq_mRNA" {sum += $7; count++} \ END {print sum / count}' -
    64.1533
    +
    64.2653

    Resources for learning AWK and sed

    @@ -2314,18 +2315,15 @@ Line

    Upcoming Data Science Training Program Workshops

    -

    Introduction -to Pathway Analysis
    -April 2, 2024 1:00-4:00pm PDT

    -

    Statistics -of Enrichment Analysis Methods
    -April 11-April 12, 2024 1:00-3:00pm PDT

    -

    Working on -Wynton
    -April 15, 2024 1:00-4:00pm PDT

    -

    Introduction -to Linear Mixed Effects Models
    -April 25-April 26, 2024 1:00-3:00pm PDT

    +

    Introduction +to RNA-Seq Analysis
    +February 13-February 14, 2025 1:00-4:00pm PST

    +

    Intermediate +RNA-Seq Analysis Using R
    +February 20, 2025 9:00am-12:00pm PST

    +

    Introduction +to Statistics, Experimental Design and Hypothesis Testing
    +February 24-February 25, 2025 1:00-3:00pm PST

    Complete Schedule

    diff --git a/intro-unix-command-line/Intro_to_Unix_Part_1.Rmd b/intro-unix-command-line/Intro_to_Unix_Part_1.Rmd index f433d8c..12cf8fd 100644 --- a/intro-unix-command-line/Intro_to_Unix_Part_1.Rmd +++ b/intro-unix-command-line/Intro_to_Unix_Part_1.Rmd @@ -1,7 +1,8 @@ --- -title: "Introduction to Unix Command-line - Part 1" +title: "Introduction to Unix Command-line" +subtitle: "Part 1" author: "Natalie Elphick" -date: "March 11th 2024" +date: "February 10th 2025" knit: (function(input, ...) { rmarkdown::render( input, @@ -15,7 +16,7 @@ output: ```{r, setup, include=FALSE} -knitr::opts_knit$set(root.dir = './unix_workshop_2024') +knitr::opts_knit$set(root.dir = './unix_workshop') ``` @@ -32,8 +33,8 @@ Bioinformatician I
    -**Ayushi Agrawal (TA)** -Bioinformatician III +**Reuben Thomas** +Associate Core Director # The Unix Command-line @@ -87,17 +88,17 @@ cd unix_workshop ```{r, engine='bash', eval=FALSE, results="hide", highlight=FALSE, comment=NA, echo = TRUE} -curl -L -o unix_workshop_2024.tar.gz 'https://www.dropbox.com/scl/fi/o8msrl3a1k986jvjll4mv/unix_workshop_2024.tar.gz?rlkey=m7jfkvpz0iq12zdzphq7013l5&dl=0' +curl -L -o unix_workshop.tar.gz 'https://www.dropbox.com/scl/fi/tdzpoivf7mienlenunqhf/unix_workshop.tar.gz?rlkey=6bfxnqgc5n4lgc9mc80ld75z4&dl=0' ``` ```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE} -tar -xzf unix_workshop_2024.tar.gz +tar -xzf unix_workshop.tar.gz ``` ```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE} -cd unix_workshop_2024 +cd unix_workshop ``` @@ -228,7 +229,7 @@ pwd ``` ```{r, engine='bash', eval=TRUE, results='markup', highlight=FALSE, comment=NA, echo=FALSE} -echo "/Users/your_username/unix_workshop_2024" +echo "/Users/your_username/unix_workshop" ``` - The default working directory when you log in or open a terminal is your user home directory  ~  @@ -257,7 +258,7 @@ ls -lah part_1 ## cd: move to a directory ```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA} -cd unix_workshop_2024/part_1 +cd unix_workshop/part_1 ls -l ``` @@ -410,7 +411,7 @@ access additional software/commands. - curl supports multiple protocols but the most commonly used one is HTTPS ```{r, engine='bash', eval=TRUE, results="hide", highlight=FALSE, comment=NA, echo = TRUE} -curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.109.refseq.tsv.gz +curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.113.refseq.tsv.gz ``` - `-o` gives the output file name and location @@ -575,20 +576,14 @@ https://www.surveymonkey.com/r/F75J6VZ ## Upcoming Data Science Training Program Workshops +[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8) +February 13-February 14, 2025 1:00-4:00pm PST -[Introduction to Pathway Analysis](https://gladstone.org/events/introduction-pathway-analysis-1) -April 2, 2024 1:00-4:00pm PDT - -[Statistics of Enrichment Analysis Methods](https://gladstone.org/events/statistics-enrichment-analysis-methods-0) -April 11-April 12, 2024 1:00-3:00pm PDT - -[Working on Wynton](https://gladstone.org/events/working-wynton) -April 15, 2024 1:00-4:00pm PDT - -[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models) -April 25-April 26, 2024 1:00-3:00pm PDT - +[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6) +February 20, 2025 9:00am-12:00pm PST +[Introduction to Statistics, Experimental Design and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-2) +February 24-February 25, 2025 1:00-3:00pm PST [Complete Schedule](https://gladstone.org/events?series=data-science-training-program) diff --git a/intro-unix-command-line/Intro_to_Unix_Part_2.Rmd b/intro-unix-command-line/Intro_to_Unix_Part_2.Rmd index d497308..2cab2d2 100644 --- a/intro-unix-command-line/Intro_to_Unix_Part_2.Rmd +++ b/intro-unix-command-line/Intro_to_Unix_Part_2.Rmd @@ -1,7 +1,8 @@ --- -title: "Introduction to Unix Command-line - Part 2" +title: "Introduction to Unix Command-line" +subtitle: "Part 2" author: "Natalie Elphick" -date: "March 12th 2024" +date: "February 11th 2025" knit: (function(input, ...) { rmarkdown::render( input, @@ -13,7 +14,7 @@ output: css: style.css --- ```{r, setup, include=FALSE} -knitr::opts_knit$set(root.dir = './unix_workshop_2024') +knitr::opts_knit$set(root.dir = './unix_workshop') ``` ## @@ -24,7 +25,7 @@ knitr::opts_knit$set(root.dir = './unix_workshop_2024') ## Introductions **Natalie Elphick** -Bioinformatician I +Bioinformatician II
    @@ -50,22 +51,22 @@ cd unix_workshop ```{r, engine='bash', eval=FALSE, results="hide", highlight=FALSE, comment=NA, echo = TRUE} -curl -L -o unix_workshop_2024.tar.gz 'https://www.dropbox.com/scl/fi/o8msrl3a1k986jvjll4mv/unix_workshop_2024.tar.gz?rlkey=m7jfkvpz0iq12zdzphq7013l5&dl=0' +curl -L -o unix_workshop.tar.gz 'https://www.dropbox.com/scl/fi/tdzpoivf7mienlenunqhf/unix_workshop.tar.gz?rlkey=6bfxnqgc5n4lgc9mc80ld75z4&dl=0' ``` ```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE} -tar -xzf unix_workshop_2024.tar.gz +tar -xzf unix_workshop.tar.gz ``` ```{r, engine='bash', eval=FALSE, results='markup', highlight=FALSE, comment=NA, echo = TRUE} -cd unix_workshop_2024 +cd unix_workshop ``` ```{r, engine='bash', eval=TRUE, results="hide", highlight=FALSE, comment=NA, echo = TRUE} -curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.111.refseq.tsv.gz +curl -o part_2/homo_sapiens.refseq.tsv.gz https://ftp.ensembl.org/pub/current_tsv/homo_sapiens/Homo_sapiens.GRCh38.113.refseq.tsv.gz ``` # File Compression @@ -416,26 +417,21 @@ https://www.surveymonkey.com/r/DY7K5ZY ## Upcoming Data Science Training Program Workshops +[Introduction to RNA-Seq Analysis](https://gladstone.org/events/introduction-rna-seq-analysis-8) +February 13-February 14, 2025 1:00-4:00pm PST -[Introduction to Pathway Analysis](https://gladstone.org/events/introduction-pathway-analysis-1) -April 2, 2024 1:00-4:00pm PDT - -[Statistics of Enrichment Analysis Methods](https://gladstone.org/events/statistics-enrichment-analysis-methods-0) -April 11-April 12, 2024 1:00-3:00pm PDT - -[Working on Wynton](https://gladstone.org/events/working-wynton) -April 15, 2024 1:00-4:00pm PDT - -[Introduction to Linear Mixed Effects Models](https://gladstone.org/events/introduction-linear-mixed-effects-models) -April 25-April 26, 2024 1:00-3:00pm PDT - +[Intermediate RNA-Seq Analysis Using R](https://gladstone.org/events/intermediate-rna-seq-analysis-using-r-6) +February 20, 2025 9:00am-12:00pm PST +[Introduction to Statistics, Experimental Design and Hypothesis Testing](https://gladstone.org/events/introduction-statistics-experimental-design-and-hypothesis-testing-2) +February 24-February 25, 2025 1:00-3:00pm PST [Complete Schedule](https://gladstone.org/events?series=data-science-training-program) + ```{r, engine='bash', eval=TRUE, results='markup', highlight=FALSE, comment=NA, echo=FALSE} rm part_2/example_script.sh rm part_2/homo_sapiens.refseq.tsv* diff --git a/intro-unix-command-line/unix_workshop.tar.gz b/intro-unix-command-line/unix_workshop.tar.gz new file mode 100644 index 0000000..248e4d2 Binary files /dev/null and b/intro-unix-command-line/unix_workshop.tar.gz differ diff --git a/intro-unix-command-line/unix_workshop_2024/part_1/.hidden_file.txt b/intro-unix-command-line/unix_workshop/part_1/.hidden_file.txt similarity index 100% rename from intro-unix-command-line/unix_workshop_2024/part_1/.hidden_file.txt rename to intro-unix-command-line/unix_workshop/part_1/.hidden_file.txt diff --git a/intro-unix-command-line/unix_workshop_2024/part_1/list_numbers.tsv b/intro-unix-command-line/unix_workshop/part_1/list_numbers.tsv similarity index 100% rename from intro-unix-command-line/unix_workshop_2024/part_1/list_numbers.tsv rename to intro-unix-command-line/unix_workshop/part_1/list_numbers.tsv