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Assignment Regrade #15

Open sr320 opened 1 year ago

sr320 commented 1 year ago

Please list out specific assignments you would like re-assessed. In other words I will ignore the Syllabus this week and grade any late assignments. (this week only)

List Assignment and provide URL.

scuba-sarah commented 1 year ago

Check week 4 output: https://github.com/course-fish546-2023/sarahyerrace-coursework/blob/main/assignments/output/text.file

sggarcia6 commented 1 year ago

Assignments: RP_Week05: https://github.com/course-fish546-2023/susan-compgenome/blob/master/code/README.md Week 06: https://github.com/course-fish546-2023/susan-coursework/blob/master/assignments/code/06-alignmentdata.Rmd Week 03: https://github.com/course-fish546-2023/susan-coursework/blob/master/assignments/code/03README.md

ocattau commented 1 year ago

Week 1 HW: https://github.com/course-fish546-2023/olivia-classwork/blob/main/homework/Week1.md Week 2 HW: https://github.com/course-fish546-2023/olivia-classwork/blob/main/homework/Week2.md Week 3 HW: https://github.com/course-fish546-2023/olivia-classwork/blob/main/homework/Week3.md

Week 1 assignment: https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/01-blast.Rmd Week 2 assignment: https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/02-Differential%20Gene%20Expression.Rmd Week 3 assignment: https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/03.1-blast.Rmd, https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/03.1-blast.html, https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/03.2-DESeq2.Rmd, https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/03.2-DESeq2.html Week 4 assignment: https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/04-hello.py, https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/04-job-sh.sh Week 6 assignment: https://github.com/course-fish546-2023/olivia-classwork/blob/main/assignments/code/06-RNAseq-snp.Rmd (images imbedded within Rmarkdown and in olivia-classwork output folder)

Research Progress Weeks 1-7: https://rpubs.com/ocattau/1041088

ChrisMantegna commented 1 year ago

Research Project RP Week 1 - Establish Repos RP Week 4 - Sliced Workflow through DESeq RP Week 5 - Readme Update RP Week 7 - adding it here because you're already here Compendium RPubs

Assignments Week 1 - Bash Week 1 - BLAST Week 1 has 2 assignments because I am unclear which counts, so I did both Week 3 - RPubs-DGE Week 4 - Hyak Week 6 - Alignment Week 6 - IGVfail Week 7 - adding it here because you're already here CG Motifs

SamCryan commented 1 year ago

Homeworks: HW1: https://github.com/course-fish546-2023/sam-coursework/blob/main/homework/week_01.md HW2: https://github.com/course-fish546-2023/sam-coursework/blob/main/homework/week_02.md

Research Progress: Week 1: Formulated Research Project idea

Week 2+3: Generated simulated data and created system to quickly generate a Jaccard score from a presence/absence matrix (under simulated_data_test.R)

Week 4: Worked on devloping a tool to download reference genomes and create a presence/absence matrix - used NCBI API to download one genome at a time (under download_script.R)

Week 5: Continued working on a download tool, eventually got NCBI datasets to work. Finalized the presence/absence matrix code. Prepared presentation. (under 01-ncbi_download.Rmd)

Week 6: Created a 17,022 genes x 17,056 genomes presence/absence matrix using premade code, ran some initial tests on genes of interest and saw expected correlations (genes within same operon were correlated, genes associated with central carbon metabolism were correlated with each other) (01-ncbi_download.Rmd into 02-full_matrix_test.Rmd)

Week 7: Generated a 3600 x 3600 correlation matrix with the Jaccard Similarity score of each gene-gene pair and generated heatmap, checked the (02-full_matrix_test.Rmd)

Assignments: Week 1: https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/01-blast.Rmd Week 2: https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/02-rnaseq.Rmd Week 3: https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/01-blast.2.Rmd + https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/02-rnaseq.2.Rmd Week 4: https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/04-job.sh + Output Week 6: https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/06-alignment.Rmd Week 7: https://github.com/course-fish546-2023/sam-coursework/blob/main/assignments/code/07-cgmotif.Rmd, https://rpubs.com/TheOneCalledSam/1041721

zbengt commented 1 year ago