User: shicks

gravatar for shicks
shicks50
Reputation:
50
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New User
Location:
USA/Baltimore/Johns Hopkins
Website:
https://www.stephanieh...
Twitter:
stephaniehicks
Last seen:
2 weeks, 4 days ago
Joined:
4 years, 5 months ago
Email:
s*******@jhu.edu

Assistant Professor of Biostatistics at Johns Hopkins Bloomberg School of Public Health

Posts by shicks

<prev • 6 results • page 1 of 1 • next >
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Comment: C: How to build and map to a "pre-mRNA" reference transcriptome for single nucleus
... That's fair. I wasn't sure if this was something that the authors of `tximport`, `tximeta`, `ensembldb` have come across and thought I would ask on the Bioc support site. I'm happy to withdraw my question if it's not relevant enough to this community. ...
written 5 weeks ago by shicks50
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How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
... Hi, What is the best way to create a reference transcriptome for both "pre-mRNA" and mature RNA in Bioconductor? I've got some single-nucleus RNA-seq (snRNA-seq) data (full-length transcripts from smart-seq2 plate-based protocol) and I would like to have a reference transcriptome that allows reads ...
ensembldb tximport single-cell tximeta snrna-seq written 5 weeks ago by shicks50 • updated 5 weeks ago by Robert Castelo2.3k
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unequal sample sizes in groups for testCovariate argument in dmrseq
... Hi, I have N=44 WGBS samples from purified cell types from whole blood samples. I'm interested in identifying DMRs for six purified cell types (DMR in Bcell vs else, CD4T vs else, etc), but I have unequal sample sizes in each group: > table(pheno_table$cell_type) Bcell CD4T CD8T G ...
dmrseq written 3 months ago by shicks50
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Comment: C: Hope for help about quantro and qsmooth-library size normalization
... Do you think differences in the sequencing depth are related to biological or technical variation? If it's technical, `quantro` actually performs an ANOVA to test if the medians of the distributions are different across groups. There is a parameter in `quantro` (`useMedianNormalized = TRUE`) to ma ...
written 4 months ago by shicks50
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Job: Postdoctoral Scientist position at intersection of Single-Cell Cancer Genomics, Data Science and Bioconductor Software Development
... Johns Hopkins Bloomberg School of Public Health Department of Biostatistics Post-Doctoral Fellowship Opening Positions to begin Spring or Summer 2019 Applications Due: Open until filled, applications will be reviewed on a rolling basis and those received by January 31, 2018 will receive priority. ...
cancer job genomics data science single-cell written 10 months ago by shicks50
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Comment: C: DESeq2- Size factors (median of ratios) assumptions - global adjustment normaliz
... Thanks Mike! Yes, DESeq2 also makes assumptions that might not be appropriate if you have global differences in the distributions of data. As Mike suggested, do you have spike-ins?  ...
written 14 months ago by shicks50

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Autobiographer 4.5 years ago, has more than 80 characters in the information field of the user's profile.

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