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GIven the interest in studies that involve tumor heterogeneity / subclonality, currently bcbio offers "out of the box" support for both somatic variants and CNVs. A useful metric that can be combined …
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Per #217, adding a new issue to dive deeper into this new feature
**A short description of the feature**
Extend the Atlas estimation specification feature to allow for the specification of multipl…
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I suggest that before we finalize the list of effects included in DC2 at the final DC2 checkpoint, we apply a coherent/consistent set of decision criteria. This comes out of a [slack conversation](ht…
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It would be useful to make a function or functions for downloading Integrated sample design data files (SDDF) from the ESS website. They are useful for computing sampling errors. This is [an example o…
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I have used NGMLR mapped bam files for SV calling using Sniffles (1.0.8) using the following script -
f=MA530_230211.ngmlr.sorted.bam
sniffles \
-s 3 \
--max_num_splits 7 \
--threads 16 \
--…
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You can read the current definitions of the Solid mission, vision, and values on https://github.com/solid/information/blob/master/solid-vision.md
Just to recap the meaning of each of the terms:
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We would like to discuss how best to correct richness/alpha diversity for differences in sequencing depth (total amplicons) when using the default dada2 pipeline, i.e. when using dada(, pooled = FALSE…
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It would be helpful to have a function or functions to get summary statistics around inequality and poverty. These could either be part of the existing `diagnostic_table` function or made as new funct…
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New thread.....
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Today there are several mechanisms in Atlas which provide cohort characterization: Heracles (adoption of Achilles for cohorts), Feature extraction (Generate w/ Features) and Cost & Utilization reports…