Skip to content

Commit a06e05b

Browse files
jfy133jfy133
committed
Merge branch 'main' into phylogenomics
2 parents c0d3d08 + dcc83fe commit a06e05b

File tree

266 files changed

+3471
-61514
lines changed

Some content is hidden

Large Commits have some content hidden by default. Use the searchbox below for content that may be hidden.

266 files changed

+3471
-61514
lines changed

‎README.md

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -55,7 +55,6 @@ If adding a new section chapter:
5555
7. Render the book the extensions' `Quarto: Render Book` command, or run the following
5656

5757
```bash
58-
#| eval: false
5958
quarto preview intro-to-ancient-metagenomics-book --render all --no-browser --no-watch-inputs
6059
```
6160

‎_quarto.yml

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@ book:
2323
- introduction-to-metagenomics.qmd
2424
- introduction-to-microbial-genomics.qmd
2525
- introduction-to-evolutionary-biology.qmd
26+
- introduction-to-edna.qmd
2627
- part: section-useful-skills.qmd
2728
chapters:
2829
- bare-bones-bash.qmd

‎ancient-metagenomic-pipelines.qmd

Lines changed: 85 additions & 48 deletions
Large diffs are not rendered by default.

‎assets/images/chapters/authentication/mapq.png

109 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure1.jpg

79.8 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure10.png

3.16 MB
Loading

‎assets/images/chapters/introduction-to-edna/figure2.jpg

93.1 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure3.jpg

74.2 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure4.jpg

91.9 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure5.jpg

87.6 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure6.jpg

55.1 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure7.jpg

146 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure8.jpg

40 KB
Loading

‎assets/images/chapters/introduction-to-edna/figure9.jpg

64 KB
Loading

‎assets/images/chapters/python-pandas/table_10_merged_df.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Level,
2+
0,5524,1957,Graduation,Single,58138,0,0,635,88,546,172,88,88,8,10,4,7,0,3,
3+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0,3,
4+
2,4141,1965,Graduation,Together,71613,0,0,426,49,127,111,21,42,8,2,10,4,0,3,
5+
3,6182,1984,Graduation,Together,26646,1,0,11,4,20,10,3,5,2,0,4,6,0,3,
6+
5,965,1971,Graduation,Divorced,55635,0,1,235,65,164,50,49,27,7,3,7,6,0,3,
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,
8+
481,11133,1973,PhD,YOLO,48432,0,1,322,3,50,4,3,42,7,1,6,8,0,5,
9+
482,9589,1948,PhD,Widow,82032,0,0,332,194,377,149,125,57,4,6,7,1,0,5,
10+
483,4286,1970,PhD,Single,57642,0,1,580,6,58,8,0,27,7,6,6,4,0,5,
11+
484,4001,1946,PhD,Together,64014,2,1,406,0,30,0,0,8,8,2,5,7,0,5,
12+
485,9405,1954,PhD,Married,52869,1,1,84,3,61,2,1,21,3,1,4,7,0,5,

‎assets/images/chapters/python-pandas/table_1_all_data.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
0,5524,1957,Graduation,Single,58138,0,0,635,88,546,172,88,88,8,10,4,7,0,3,11
3+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0,3,11
4+
2,4141,1965,Graduation,Together,71613,0,0,426,49,127,111,21,42,8,2,10,4,0,3,11
5+
3,6182,1984,Graduation,Together,26646,1,0,11,4,20,10,3,5,2,0,4,6,0,3,11
6+
4,7446,1967,Master,Together,62513,0,1,520,42,98,0,42,14,6,4,10,6,0,3,11
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…
8+
1749,9432,1977,Graduation,Together,666666,1,0,9,14,18,8,1,12,3,1,3,6,0,3,11
9+
1750,8372,1974,Graduation,Married,34421,1,0,3,3,7,6,2,9,1,0,2,7,0,3,11
10+
1751,10870,1967,Graduation,Married,61223,0,1,709,43,182,42,118,247,9,3,4,5,0,3,11
11+
1752,7270,1981,Graduation,Divorced,56981,0,0,908,48,217,32,12,24,2,3,13,6,0,3,11
12+
1753,8235,1956,Master,Together,69245,0,1,428,30,214,80,30,61,6,5,10,3,0,3,11

‎assets/images/chapters/python-pandas/table_2_all_data_head.csv

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
0,5524,1957,Graduation,Single,58138,0,0,635,88,546,172,88,88,8,10,4,7,0,3,11
3+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0,3,11
4+
2,4141,1965,Graduation,Together,71613,0,0,426,49,127,111,21,42,8,2,10,4,0,3,11
5+
3,6182,1984,Graduation,Together,26646,1,0,11,4,20,10,3,5,2,0,4,6,0,3,11
6+
4,7446,1967,Master,Together,62513,0,1,520,42,98,0,42,14,6,4,10,6,0,3,11

‎assets/images/chapters/python-pandas/table_3_all_data_first_2_lines.csv

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,3 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0,3,11
3+
2,4141,1965,Graduation,Together,71613,0,0,426,49,127,111,21,42,8,2,10,4,0,3,11

‎assets/images/chapters/python-pandas/table_4_all_data_conditional_subset.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
0,5524,1957,Graduation,Single,58138,0,0,635,88,546,172,88,88,8,10,4,7,0,3,11
3+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0,3,11
4+
18,7892,1969,Graduation,Single,18589,0,0,6,4,25,15,12,13,2,1,3,7,0,3,11
5+
20,5255,1986,Graduation,Single,NaN,1,0,5,1,3,3,263,362,27,0,0,1,0,3,11
6+
33,1371,1976,Graduation,Single,79941,0,0,123,164,266,227,30,174,2,4,9,1,0,3,11
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…
8+
1720,10968,1969,Graduation,Single,57731,0,1,266,21,300,65,8,44,8,8,6,6,0,3,11
9+
1723,5959,1968,Graduation,Single,35893,1,1,158,0,23,0,0,18,3,1,5,8,0,3,11
10+
1743,4201,1962,Graduation,Single,57967,0,1,229,7,137,4,0,91,4,2,8,5,0,3,11
11+
1746,7004,1984,Graduation,Single,11012,1,0,24,3,26,7,1,23,3,1,2,9,0,3,11
12+
1748,8080,1986,Graduation,Single,26816,0,0,5,1,6,3,4,3,0,0,3,4,0,3,11

‎assets/images/chapters/python-pandas/table_5_all_data_conditional_subset2.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
26,10738,1951,Master,Single,49389,1,1,40,0,19,2,1,3,2,0,3,7,0,3,11
3+
46,6853,1982,Master,Single,75777,0,0,712,26,538,69,13,80,3,6,11,1,0,3,11
4+
76,11178,1972,Master,Single,42394,1,0,15,2,10,0,1,4,1,0,3,7,0,3,11
5+
98,6205,1967,Master,Single,32557,1,0,34,3,29,0,4,10,2,1,3,5,0,3,11
6+
110,821,1992,Master,Single,92859,0,0,962,61,921,52,61,20,5,4,12,2,0,3,11
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…
8+
1690,3520,1990,Master,Single,91172,0,0,162,28,818,0,28,56,4,3,7,3,0,3,11
9+
1709,4418,1983,Master,Single,89616,0,0,671,47,655,145,111,15,7,5,12,2,0,3,11
10+
1714,2980,1952,Master,Single,8820,1,1,12,0,13,4,2,4,3,0,3,8,0,3,11
11+
1738,7366,1982,Master,Single,75777,0,0,712,26,538,69,13,80,3,6,11,1,0,3,11
12+
1747,9817,1970,Master,Single,44802,0,0,853,10,143,13,10,20,9,4,12,8,0,3,11

‎assets/images/chapters/python-pandas/table_6_Describing_df.csv

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,9 @@
1+
,ID,Year_Birth,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
count,1754,1754,1735,1754,1754,1754,1754,1754,1754,1754,1754,1754,1754,1754,1754,1754,1754,1754
3+
mean,5584.696123,1969.571266,51166.5781,0.4561,0.480616,276.072406,28.034778,166.492018,40.517104,28.958381,47.266819,3.990878,2.576967,5.714937,5.332383,0.011403,3,11
4+
std,3254.655979,11.876614,26200.41918,0.537854,0.536112,314.604735,41.348883,225.561694,57.412986,42.83066,53.885647,2.708278,2.848335,3.231465,2.380183,0.106202,0,0
5+
min,0,1893,1730,0,0,0,0,0,0,0,0,0,0,0,0,0,3,11
6+
25%,2802.5,1960,33574.5,0,0,19,2,15,3,2,10,2,0,3,3,0,3,11
7+
50%,5468,1971,49912,0,0,160.5,9,66,13,9,27,3,1,5,6,0,3,11
8+
75%,8441.25,1978,68130,1,1,454,35,232,53.5,35,63,6,4,8,7,0,3,11
9+
max,11191,1996,666666,2,2,1492,199,1725,259,263,362,27,28,13,20,1,3,11

‎assets/images/chapters/python-pandas/table_7_isna_df.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
0,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
3+
1,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
4+
2,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
5+
3,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
6+
4,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…
8+
1749,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
9+
1750,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
10+
1751,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
11+
1752,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE
12+
1753,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE,FALSE

‎assets/images/chapters/python-pandas/table_8_concat_df.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain,Z_CostContact,Z_Revenue
2+
0,5524,1957,Graduation,Single,58138,0,0,635,88,546,172,88,88,8,10,4,7,0,3,11
3+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0,3,11
4+
2,4141,1965,Graduation,Together,71613,0,0,426,49,127,111,21,42,8,2,10,4,0,3,11
5+
3,6182,1984,Graduation,Together,26646,1,0,11,4,20,10,3,5,2,0,4,6,0,3,11
6+
4,7446,1967,Master,Together,62513,0,1,520,42,98,0,42,14,6,4,10,6,0,3,11
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…
8+
481,11133,1973,PhD,YOLO,48432,0,1,322,3,50,4,3,42,7,1,6,8,0,3,11
9+
482,9589,1948,PhD,Widow,82032,0,0,332,194,377,149,125,57,4,6,7,1,0,3,11
10+
483,4286,1970,PhD,Single,57642,0,1,580,6,58,8,0,27,7,6,6,4,0,3,11
11+
484,4001,1946,PhD,Together,64014,2,1,406,0,30,0,0,8,8,2,5,7,0,3,11
12+
485,9405,1954,PhD,Married,52869,1,1,84,3,61,2,1,21,3,1,4,7,0,3,11

‎assets/images/chapters/python-pandas/table_9_doncat_drop_df.csv

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
,ID,Year_Birth,Education,Marital_Status,Income,Kidhome,Teenhome,MntWines,MntFruits,MntMeatProducts,MntFishProducts,MntSweetProducts,MntGoldProds,NumWebPurchases,NumCatalogPurchases,NumStorePurchases,NumWebVisitsMonth,Complain
2+
0,5524,1957,Graduation,Single,58138,0,0,635,88,546,172,88,88,8,10,4,7,0
3+
1,2174,1954,Graduation,Single,46344,1,1,11,1,6,2,1,6,1,1,2,5,0
4+
2,4141,1965,Graduation,Together,71613,0,0,426,49,127,111,21,42,8,2,10,4,0
5+
3,6182,1984,Graduation,Together,26646,1,0,11,4,20,10,3,5,2,0,4,6,0
6+
4,7446,1967,Master,Together,62513,0,1,520,42,98,0,42,14,6,4,10,6,0
7+
…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…,…
8+
481,11133,1973,PhD,YOLO,48432,0,1,322,3,50,4,3,42,7,1,6,8,0
9+
482,9589,1948,PhD,Widow,82032,0,0,332,194,377,149,125,57,4,6,7,1,0
10+
483,4286,1970,PhD,Single,57642,0,1,580,6,58,8,0,27,7,6,6,4,0
11+
484,4001,1946,PhD,Together,64014,2,1,406,0,30,0,0,8,8,2,5,7,0
12+
485,9405,1954,PhD,Married,52869,1,1,84,3,61,2,1,21,3,1,4,7,0

‎assets/references/index.bib

Lines changed: 35 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
@article{Marchesi2015-pj,
2+
title = {The vocabulary of microbiome research: a proposal},
3+
author = {Marchesi, Julian R and Ravel, Jacques},
4+
journal = {Microbiome},
5+
publisher = {Springer Nature},
6+
volume = 3,
7+
number = 1,
8+
pages = 31,
9+
abstract = {The advancement of DNA/RNA, proteins, and metabolite analytical
10+
platforms, combined with increased computing technologies, has
11+
transformed the field of microbial community analysis. This
12+
transformation is evident by the exponential increase in the
13+
number of publications describing the composition and structure,
14+
and sometimes function, of the microbial communities inhabiting
15+
the human body. This rapid evolution of the field has been
16+
accompanied by confusion in the vocabulary used to describe
17+
different aspects of these communities and their environments.
18+
The misuse of terms such as microbiome, microbiota, metabolomic,
19+
and metagenome and metagenomics among others has contributed to
20+
misunderstanding of many study results by the scientific
21+
community and the general public alike. A few review articles
22+
have previously defined those terms, but mainly as sidebars, and
23+
no clear definitions or use cases have been published. In this
24+
editorial, we aim to propose clear definitions of each of these
25+
terms, which we would implore scientists in the field to adopt
26+
and perfect.},
27+
month = jul,
28+
year = 2015,
29+
url = {https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-015-0094-5},
30+
doi = {10.1186/s40168-015-0094-5},
31+
pmc = {PMC4520061},
32+
pmid = 26229597,
33+
issn = {2049-2618,2049-2618},
34+
language = {en}
35+
}

0 commit comments

Comments
 (0)