dib-lab 2020-ibd issues

dib-lab / 2020-ibd

Analysis of publicly available metagenomic sequencing data from humans with IBD.

BSD 3-Clause "New" or "Revised" License

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issues

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Updates figure 6 upset plot about shared k-mers

#32 taylorreiter closed 2 years ago
0
woops rule all

#31 taylorreiter closed 2 years ago
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Paper cleanup

#30 taylorreiter closed 2 years ago
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multiqc env version

#29 taylorreiter opened 2 years ago
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[WIP] rearrange charcoal so runs all at once

#28 taylorreiter closed 3 years ago
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fix charcoal conf

#27 taylorreiter closed 3 years ago
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charcoal needs to be run with `-j 1` to work appropriately in this Snakefile

#26 taylorreiter closed 3 years ago
1
Collapse vita rules that were duplicated when "seed" was added as a var

#25 taylorreiter closed 3 years ago
0
[WIP] Update pipeline to accomodate SGC updates and to streamline rules

#24 taylorreiter closed 3 years ago
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reference: iMOKA: k-mer based software to analyze large collections of sequencing data

#23 ctb opened 3 years ago
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reference: "Bridging the gap between k-mers and genetic events"

#22 ctb opened 3 years ago
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mrg master into update pipeline

#21 taylorreiter closed 3 years ago
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Misc suggestions

#20 ctb closed 3 years ago
1
add 16s singlem rule, eggnog for multifasta queries, and update multifasta query conf

#19 taylorreiter closed 3 years ago
0
record eggnog database download command

#18 taylorreiter opened 4 years ago
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Add rules to combine sgc pangenome sigs, run gather, and calc stats on results

#17 taylorreiter closed 4 years ago
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Add rules to run kofamscan on the significantly differentially abundant amino acid sequences

#16 taylorreiter closed 4 years ago
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Corncob

#15 taylorreiter closed 4 years ago
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remove checkpoints, add corncob script as three sep pieces

#14 taylorreiter closed 4 years ago
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reorg envs to be in separate folder

#13 taylorreiter closed 4 years ago
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Digiplass

#12 taylorreiter closed 4 years ago
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fix feather-format and pyarrow versions

#11 taylorreiter opened 4 years ago
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change sgc queries to double checkpoint

#10 taylorreiter closed 4 years ago
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update appendix outline

#9 taylorreiter closed 4 years ago
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update doc new study model and sgc res

#8 taylorreiter closed 4 years ago
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Add rules to find and compare genomes predicted to be important in 5 of 6 models

#7 taylorreiter closed 4 years ago
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add lib size and n hashes to permanova

#6 taylorreiter closed 4 years ago
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misc sandbox script updates

#5 taylorreiter closed 4 years ago
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overhaul pipeline

#4 taylorreiter closed 4 years ago
0
fix ihmp download rule

#3 taylorreiter opened 4 years ago
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Fix link

#2 luizirber closed 4 years ago
0
sourmash version for abundance preservation during signature intersection

#1 taylorreiter opened 4 years ago
2