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**Authors:** Fiona C. Wood, Yonas I. Tekle
**Abstract:** The advent of molecular phylogenetics has led to numerous cases where species determination differs based on molecular or morphological data. …
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Sparse input matrix (30k cells x 6000 genes, single-cell sequencing data, with 35 labels for the cells) produces nan's in the loss function during training.
Adding a small epsilon, 1e-12, to the soft…
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### Report
hi, I have encounter issues with the estimation of CGC substrate abundance and CGC abundance.
I followed all the steps from the manual and it ran smoothly, including dbcan_utils fam_abu…
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Hello,
I am a Master Student and currently working on creating a pangenome from 21 longread accessions. A lot of my ideas on how to create my pan gene library was inspired by your work, so thanks in …
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In attempting to use SURVIVOR_ant in chicken annotation. I provided the GFF(Gallus_gallus.GRCg6a.98.gff3.gz) file VCF(gallus_gallus.vcf.gz) file and bed file(galGal6_ens_whole_gene.bed) from ensemblor…
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@DarioS moving over from email to issue tracker:
If there are more than two copy number levels for a gene, CNVRanger does an ANOVA-like test, which is a test for differences in means. Is there a wa…
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In this issue we'd like to discuss what to do with Gene IDs.
In the model currently, there are general gene IDs come from Beata's original sequencing (e.g. `RTMO03744` However, since then any reac…
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Hello,
I am analyzing some RNA samples and I have noticed an issue with the quantification part using Star.
The data I have was generated by an external company using TruSeq3-PE-2 library, which…
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We have methods for associating individual genetic variants and phenotypes (https://github.com/pystatgen/sgkit/pull/16, https://github.com/pystatgen/sgkit/pull/66), but inferring associations with gen…
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May i ask 1 question:
if data is already pseudobulk object from scRNAseq data with logCPM value, how can i change it back to a seurat object with counts value? Can i still use above method to turn …