The rnorm_multi() function makes multiple normally distributed vectors with specified parameters and relationships.
https://cran.r-project.org/web/packages/faux/vignettes/rnorm_multi.html
Tuesday, August 31, 2021
simulated correlated random values in R
SGRP sanger yeast resequecing data download
http://www.moseslab.csb.utoronto.ca/sgrp/download.html
Data from Bergström et al. (2014)
Download the new SGRP sequences here
Download the annotations for the new SGRP here
Download the loss of function variants for the new SGRP here
Download the SIFT prediction for SNPs here
Download the reads here
Download the S. cerevisiae reference-based SNP calls and strain genotypes here
Download the S. paradoxus reference-based SNP calls and strain genotypes here
Download the new SGRP sequences here
Download the annotations for the new SGRP here
Download the loss of function variants for the new SGRP here
Download the SIFT prediction for SNPs here
Download the reads here
Download the S. cerevisiae reference-based SNP calls and strain genotypes here
Download the S. paradoxus reference-based SNP calls and strain genotypes here
Monday, August 30, 2021
cpsc4180 Aug 30, Google mobility and covid19 analysis
== pre-class to do:
calendar email invitation: done
socrative questions (questions on contents from last lecture ):
update Canvas course materials, update learning objectives. assignments as needed: done
Test-run code: Rmd -> HTML report with content. done
* GitHub has a connection problem today due to hurrican Ida?!. So, we have to download the jhu data manually. *
== In-class to do:
clean up destktop space, calendars,
ZOOM, live transcript (start video recording).
Socrative sign in
Review Chapter 2
R-COVID19 Chapter 3. Google Mobility.
Only one student was in-person today, an Amy veteran.
Thursday, August 26, 2021
MS thesis, fall 2021, important dates
- Fall Primary Graduation Deadlines for Master Students.
- Oct 1- Last day to schedule your defense
- Oct 15- Last day to defend your thesis
- Nov 1- Deadline to submit thesis and thesis exam results for Dec. Graduation.
- Nov 30- Last day for final edits to be submitted and accepted as requested by graduate school.
- Dec 10- Graduate Student Commencement.
Sanger yeast sequencing project
https://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html
Where is SNP matrix?
Wednesday, August 25, 2021
R heatmap references
https://jokergoo.github.io/ComplexHeatmap-reference/book/index.html
https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#colors
cpsc4180 data science programming, Day 4, August 25, R Covid, Chapter 2
== pre-class to do:
calendar email invitation: done
socrative questions (data camp, have you checked into course canvas site? basic R and data bias questions from last lecture ); done
update Canvas course materials, update learning objectives. assignments as needed.
Test-run code: Rmd -> HTML report with content
== In-class to do:
clean up destktop space, calendars,
ZOOM, live transcript (start video recording).
Socrative sign in
Review Chapter 1
R-COVID19 Chapter 2. Qin went through this chapter in about 30 mintues, then asked student to modify the code to look at different counties for about 20 minutes.
In the remaining 20 minutes, Qin posed some more challenging questions: How to find weird counties and weird states. This question is not clear to students, because their picked weird counties names like "whitefield". So, the weirdness was interpreted by the students as in the literacy sense not as computer science or data science.
A student reminded me that homework assignment on Canvas does automatically showed on the modules, So, I have manually put them there, even though they show up in Canvas Calendars.
Tuesday, August 24, 2021
SFS jobs
https://www.ziprecruiter.com/c/Tennessee-Valley-Authority/Job/Analyst,-Cybersecurity-511763/-in-Chattanooga,TN?jid=813d5b8dc243b15f&lvk=b7FPSZvocsofEH8OGaoYaA.--M9GzCimh-
https://www.teksystems.com/en/locations
Term II, Fall 2021 course for incoming PhD student
TERM 2 fall 2021 courses,
Term II start on Oct 4. 10days before Sep 23.
Monday, August 23, 2021
WORD problem
Someone inadvertently add some blank lines into the header in WORD, probably online, which pushed my text down.
cpsc 4180 8/23 Day 3, R-covid chapter 1
== pre-class to do:
calendar email invitation
socrative questions (datacamp, R RStudio installation, datacamp registration and assignment)
update Canvas course materials, update learning objectives. assignments as needed.
Test-run code: Rmd -> HTML report with content
== In-class to do:
ZOOM, live transcript (start video recording).
Socrative sign in
Review simple R, on CoLab and Rstudio Cloud.
R-COVID19 Rmd code. Prepare to finish Chapter 1.
Sunday, August 22, 2021
GA adertisement
Graduate researcher positions are available to apply data science and machine learning to predict new coronavirus variants, develop interpretable deep learning methods to predict biological clocks and diseases. Candidates are expected to code in R and/or Python and have good writing skills. Our group’s recent publications appeared in Scientific Reports, GeroScience, and BMC Bioinformatics. Students from all backgrounds are welcome, as long as they have strong interests in the multi-disciplinary research projects and have sufficient skills. To apply, please send your resume, transcripts, and relevant supporting materials such as past coding projects or essays to hong-qin@utc.edu
Friday, August 20, 2021
Thursday, August 19, 2021
ratg13 vs RmYN sequences
hqin@ECS323GPUStation:~$ mummer -maxmatch -n -l 100 ratg13.fasta RmYn.fasta
# reading input file "ratg13.fasta" of length 29855
# construct suffix tree for sequence of length 29855
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# CONSTRUCTIONTIME mummer ratg13.fasta 0.01
# reading input file "RmYn.fasta" of length 146512
# matching query-file "RmYn.fasta"
# against subject-file "ratg13.fasta"
> hCoV-19/bat/Yunnan/RmYN05/2020|EPI_ISL_1699445|2020-05-25
29642 29492 177
> hCoV-19/bat/Yunnan/RmYN07/2020|EPI_ISL_1699447|2020-06-03
15034 14968 119
26254 26098 126
29670 29542 149
> hCoV-19/bat/Yunnan/RmYN08/2020|EPI_ISL_1699448|2020-07-14
29642 29492 177
> hCoV-19/bat/Yunnan/RmYN01/2019|EPI_ISL_412976|2019-06-25
> hCoV-19/bat/Yunnan/RmYN02/2019|EPI_ISL_412977|2019-06-25
175 163 150
782 770 116
2938 2926 102
4211 4196 113
5666 5651 104
6356 6341 153
7166 7151 119
7301 7286 107
7469 7454 122
8207 8192 110
9572 9557 123
10854 10839 112
11540 11525 107
12017 12002 173
12608 12593 164
12821 12806 149
13199 13184 125
13325 13310 193
13621 13606 113
13735 13720 107
13918 13903 111
14380 14365 104
14846 14831 133
15001 14986 116
15401 15386 115
15595 15580 116
16084 16069 122
16564 16549 158
16766 16751 118
16937 16922 214
17452 17437 194
17770 17755 116
19093 19078 125
20347 20332 104
25304 25162 108
25413 25271 118
25702 25560 104
26089 25947 164
26254 26112 155
28639 28488 122
29284 29133 104
29461 29310 180
29648 29497 171
RaTG13
Bat coronavirus RaTG13, complete genome
GenBank: MN996532.2
https://www.ncbi.nlm.nih.gov/nuccore/1916859392
align seq mummer on ecs323gpustation
Had trouble to compile mummer4
Installed mummer3.23 from its binary
this worked:
$ mummer -maxmatch -n -l 100 ratg13.fasta prC31.fasta > ratg13-prc31.mumm
hqin@ECS323GPUStation:~$ cat ratg13-prc31.mumm
> hCoV-19/bat/Yunnan/PrC31/2018|EPI_ISL_1098866|2018-08
1103 1065 140
4211 4173 158
5666 5628 104
6399 6361 103
7160 7122 113
7301 7263 107
7469 7431 122
7607 7569 119
10854 10816 142
11957 11919 233
12320 12282 131
26317 26209 115
27959 27858 109
28480 28379 101
28666 28565 110
29266 29165 124
29461 29360 155
29708 29606 111
> hCoV-19/Wuhan/WH01/2019|EPI_ISL_406798|2019-12-26
191 166 134
4291 4269 120
5728 5706 105
6734 6712 146
7160 7138 104
7739 7717 101
8159 8137 104
10484 10462 106
10854 10832 124
11522 11500 107
12320 12298 116
12608 12586 204
12813 12791 157
13325 13303 193
13621 13599 113
13735 13713 107
13918 13896 111
14263 14241 116
14485 14463 111
14626 14604 158
14845 14823 134
15001 14979 203
15373 15351 143
15595 15573 116
15811 15789 113
16132 16110 179
16342 16320 137
16723 16701 140
16903 16881 104
17152 17130 146
19093 19071 335
20938 20916 116
21908 21886 131
25840 25830 119
26038 26028 115
26154 26144 162
26317 26307 200
27117 27110 132
27742 27736 139
28151 28145 127
28480 28474 101
28585 28579 203
29500 29494 141
hqin@ECS323GPUStation:~$ mummer -maxmatch -n -l 200 ratg13.fasta ncbi-ref.fasta > ratg-ncib.mumm
# reading input file "ratg13.fasta" of length 29855
# construct suffix tree for sequence of length 29855
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# CONSTRUCTIONTIME mummer ratg13.fasta 0.01
# reading input file "ncbi-ref.fasta" of length 29903
# matching query-file "ncbi-ref.fasta"
# against subject-file "ratg13.fasta"
# COMPLETETIME mummer ratg13.fasta 0.01
# SPACE mummer ratg13.fasta 0.06
hqin@ECS323GPUStation:~$ cat ratg-ncib.mumm
> NC_045512.2
12608 12611 204
15001 15004 203
19093 19096 335
26317 26332 200
28585 28604 203
hqin@ECS323GPUStation:~$ mummer -maxmatch -n -l 200 ncbi-ref.fasta ratg13.fasta > ncbi-ratg.mumm
# reading input file "ncbi-ref.fasta" of length 29903
# construct suffix tree for sequence of length 29903
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# CONSTRUCTIONTIME mummer ncbi-ref.fasta 0.01
# reading input file "ratg13.fasta" of length 29855
# matching query-file "ratg13.fasta"
# against subject-file "ncbi-ref.fasta"
# COMPLETETIME mummer ncbi-ref.fasta 0.01
# SPACE mummer ncbi-ref.fasta 0.06
hqin@ECS323GPUStation:~$ cat ncbi-ratg.mumm
> hCoV-19/bat/Yunnan/RaTG13/2013|EPI_ISL_402131|2013-07-24
12611 12608 204
15004 15001 203
19096 19093 335
26332 26317 200
28604 28585 203
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