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Some of these are more science or data analysis errors rather then reproducibility, but it is what I found from looking around for a few hours.
- Incorrect encoding of binary variable: https://jama…
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The README.md claims one can run tigmint with any number of threads.
It turn out the maximum at least in some step is just 6:
`long-to-linked-pe v1.0: Using more than 6 threads does not scale, r…
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Our lab is doing the in-house sequencing now with ONT and we have to report our results on a routine basis.
One of the requirements is that we have to submit the untrimmed BAM file as noted here, …
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I've been working a lot with precomputed distance matrices lately. The option to use these precomputed distances in `umap.umap_.fuzzy_simplicial_set` would be really helpful.
**Is this possible wi…
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Today talking with some nf-core Nextflow developers, it came up that it would be useful to be able to output a processed PEP, either in CSV format or in yaml/json format.
So, think of it as a PEP …
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Running covigator-ngs-pipeline with 2 fastq files returns error message and does not create vcf file.
It does create these 5 files as expected:
4014963632_S9.coverage.tsv
4014963632_S9.deduplicati…
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## Potential Delta (AY.4) and Omicron recombinant
## **Description**
**Sub-lineage of**: AY.4
**Earliest sequence**: 2022-01-17 (France | EPI_ISL_9959921 | EPI_ISL_9879436)
**Most recent …
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### Abstract
This workshop will provide a beginner’s guide to matrix factorization, principal component analysis (PCA), the difference between singular value decomposition, different forms of PCA and…
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Hi,
I have incorporated Bowtie2 into my Hi-C pipeline HiCUP (https://www.bioinformatics.babraham.ac.uk/projects/hicup/). I have received an email from a HiCUP user stating that Bowtie2 fails when…
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Recent work -- (Gu, et al., 2020; "PubMedBERT") and (Veysel and Talby, 2020) -- seems to show that OOVs (writ large, meaning what your word-level vocabulary is or is not) are detrimental to NER perfor…