malariagen ag1000g-phase3-data-paper issues

malariagen / ag1000g-phase3-data-paper

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bug in calculation of location-colours

#75 leehart opened 2 years ago
2
accessibility and SNP discovery work

#74 hardingnj closed 3 years ago
0
66 snp discovery

#73 hardingnj closed 3 years ago
1
iterate on text

#72 hardingnj closed 3 years ago
0
70 improve accessibility text

#71 hardingnj closed 3 years ago
1
Improve text around genome accessibility

#70 hardingnj opened 3 years ago
0
Text and code around site filter eval

#69 hardingnj closed 3 years ago
1
iterate text on results

#68 hardingnj closed 3 years ago
0
update sample qc summary notebook

#67 hardingnj closed 3 years ago
1
SNP discovery

#66 hardingnj opened 3 years ago
0
Improve results text: re sample QC

#65 hardingnj closed 3 years ago
0
Insecticide resistance

#64 hardingnj opened 3 years ago
0
Gene drive results

#63 hardingnj opened 3 years ago
0
PCA results

#62 hardingnj opened 3 years ago
0
Improve results text re: site filtering

#61 hardingnj closed 3 years ago
0
Improve results text re: coverage

#60 hardingnj opened 3 years ago
0
aim plots for gamb_colu vs arab and gamb vs colu

#59 hardingnj closed 3 years ago
1
WIP - UMAP Figure - FOR DISCUSSION

#58 cclarkson closed 3 years ago
3
Consolidate methods

#57 hardingnj closed 3 years ago
3
Confusing name in PCA data

#56 alimanfoo opened 3 years ago
0
Population definitions suggestions

#55 alimanfoo opened 3 years ago
0
WIP for cc overview

#54 hardingnj closed 3 years ago
2
Error during Build Manuscript step in Manubot workflow, running filter pandoc-manubot-cite

#53 leehart opened 3 years ago
5
Merge upstream Manubot rootstock

#52 leehart closed 3 years ago
1
initial pass at AIM plots (q98)

#51 hardingnj closed 3 years ago
1
Upgrade Manubot workflow to use conda-incubator/setup-miniconda@v2

#50 leehart closed 3 years ago
1
Q96 introgression

#49 hardingnj closed 3 years ago
1
Manubot workflow run failure

#48 leehart closed 3 years ago
4
Re-calc location colours using CIELAB colour space

#47 leehart closed 3 years ago
22
Builds sample/site location table csv and READMEs

#46 cclarkson closed 3 years ago
1
Convert ag3.py to use intake where poss. Add nb to check module.

#45 leehart closed 3 years ago
1
Produce location colours. Store as YAML. Make available as dict from ag3.py

#44 leehart closed 3 years ago
4
Computation of genetic diversity stats and comparison between populations

#43 jonbrenas opened 3 years ago
14
Add sample_names and rename

#42 hardingnj closed 3 years ago
1
Add nb to calc, store PCA data

#41 leehart closed 3 years ago
6
new crosses meta data has fewer samples than crosses genotypes

#40 cclarkson closed 3 years ago
1
ag3.py does not pull down the new crosses meta data

#39 cclarkson opened 3 years ago
1
Add relocated output files

#38 hardingnj closed 3 years ago
1
q13PCA figure: Includes creation of population groups.

#37 hardingnj closed 3 years ago
22
q41 add text re: wild sample and crosses.

#36 hardingnj closed 3 years ago
4
Add allele counts cloud storage option

#35 leehart closed 3 years ago
10
Create allele counts for PCA/UMAP

#34 cclarkson closed 3 years ago
21
WIP Q41/2/4/5 Sampling results/methods text

#33 cclarkson closed 3 years ago
2
phase 3 crosses meta data - release bucket version incorrect

#32 cclarkson closed 3 years ago
3
q6 Add pipeline to create allele count arrays

#31 hardingnj closed 3 years ago
4
tidy data and content/tables

#30 hardingnj closed 3 years ago
5
Add exome calculations

#29 hardingnj closed 3 years ago
1
WIP notebook to report species counts and fractions

#28 hardingnj opened 3 years ago
1
Split methods and add text around accessibility/peformance of site filters

#27 hardingnj closed 3 years ago
2
add text around species assignment

#26 hardingnj closed 3 years ago
2