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sanjaynagi
/
AmpSeeker
A snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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implement stable cross-nb colours
#147
sanjaynagi
closed
2 weeks ago
1
assign colours in workflow to metadata cohort cols, use for plotting throughout
#146
sanjaynagi
closed
2 weeks ago
0
AmpSeeker struggles to be re-run
#145
sanjaynagi
opened
3 weeks ago
0
rename sampleID to sample_id
#144
sanjaynagi
closed
3 weeks ago
0
sample PCA / NJT outlier removal
#143
sanjaynagi
closed
3 weeks ago
1
harmonise all dataframe naming
#142
sanjaynagi
opened
3 weeks ago
0
add pca outlier removal (sample QC)
#141
sanjaynagi
closed
3 weeks ago
1
miscellaneous small fixes, add AD info to VCF, improve aims plot
#140
sanjaynagi
closed
3 weeks ago
0
not all samples showing in qc nbs
#139
sanjaynagi
closed
3 weeks ago
0
scales on the plate statistics nb
#138
sanjaynagi
closed
3 weeks ago
0
check variant calling with GH2017 GAARD sample set
#137
sanjaynagi
closed
3 weeks ago
1
species id - check exact alt alleles
#136
sanjaynagi
closed
1 month ago
0
add exact alleles to bed 14-10-24
#135
sanjaynagi
closed
1 month ago
0
implement checks for exact alleles
#134
sanjaynagi
opened
1 month ago
1
add neighbour joining tree
#133
sanjaynagi
closed
1 month ago
1
add njt and diplotype clustering
#132
sanjaynagi
closed
1 month ago
0
Increase markdown text of notebooks
#131
sanjaynagi
opened
1 month ago
0
Bug fixes
#130
sanjaynagi
closed
1 month ago
0
fix demultiplex stats input requirement
#129
sanjaynagi
closed
1 month ago
0
Diplotype clustering of each amplicon
#128
sanjaynagi
closed
1 month ago
1
add exact alleles to bed file
#127
sanjaynagi
closed
1 month ago
0
add support for custom snpeff dbs
#126
sanjaynagi
closed
4 months ago
1
support for custom snpEff db generation
#125
sanjaynagi
closed
4 months ago
0
bug in sample_quality_control
#124
sanjaynagi
closed
1 month ago
1
add contributor information to docs
#123
sanjaynagi
opened
5 months ago
0
bcl_output should be in results
#122
sanjaynagi
closed
1 month ago
0
Create _toc from _toc_skeleton in process_toc.ipynb
#121
sanjaynagi
closed
6 months ago
1
prevent adding ag-vampir notebooks to _toc.yml if they are present
#120
sanjaynagi
closed
6 months ago
0
update docs and add example sample sheet
#119
sanjaynagi
closed
6 months ago
0
multiallelic sites allele freq calc is wrong
#118
sanjaynagi
closed
9 months ago
1
fixes and improvements
#117
sanjaynagi
closed
9 months ago
0
Implement a run information and run statistics notebook, update ag-vampir.bed
#116
sanjaynagi
closed
9 months ago
0
nb for sample metadata/general run information
#115
sanjaynagi
closed
9 months ago
0
Assign taxon to metadata
#114
sanjaynagi
closed
9 months ago
1
speed up snp-dataframe nb
#113
sanjaynagi
closed
9 months ago
2
Improve allele frequencies
#112
sanjaynagi
closed
9 months ago
2
enable multiple cohort columns
#111
sanjaynagi
closed
9 months ago
1
show frequencies of all ALTs
#110
sanjaynagi
closed
9 months ago
1
update logo
#109
sanjaynagi
closed
9 months ago
0
assign taxon with species id notebook
#108
sanjaynagi
closed
9 months ago
0
a single cohort_columns config option for all analyses
#107
sanjaynagi
closed
9 months ago
1
sample-qc infrastructure
#106
sanjaynagi
closed
9 months ago
0
genetic diversity
#105
sanjaynagi
closed
9 months ago
0
Testing - use whole reference genome from Vectorbase
#104
sanjaynagi
closed
9 months ago
0
testing - replace mini reference with full AgamP4 reference.
#103
sanjaynagi
closed
9 months ago
0
Added kdr origins notebook
#102
EricRLucas
closed
9 months ago
11
primer-rebalancing
#101
sanjaynagi
closed
10 months ago
0
Improve snp-dataframe-excel functions
#100
sanjaynagi
closed
10 months ago
0
update docs
#99
sanjaynagi
opened
11 months ago
0
Diplotype clustering tree of samples
#98
sanjaynagi
closed
1 month ago
2
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