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Comment: How to filter columns in a raw sparse matrix in R
by
bk11
★
2.3k
You can do this-
good_cells <-c(all_good_cells_rhemac10$V1)
combined_rhemac10_count_matrix_good_cells <- combined_rhemac10_count_m…
Comment: Integration of transcriptomics and proteomics: difficult matching names
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ntsopoul
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you are right! Excel just did not find it...
Answer: Integration of transcriptomics and proteomics: difficult matching names
by
ntsopoul
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I found a good solution but it is really cumbersome.
I use UniProt.ws to derive unique gene names (readable names) and also ambiguous name…
Comment: Merging Outputs from plink --assoc and --hardy to Produce Table
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Koketso
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Thank you so much. How about calculating allelic odds ratios? Which plink/R command can I use for that?
Comment: Integration of transcriptomics and proteomics: difficult matching names
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ATpoint
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For such analysis I always first translate everything to Ensembl Gene IDs (biomaRt is a good help here) and then I do the matching with thi…
Comment: Integration of transcriptomics and proteomics: difficult matching names
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I can see this in the list
GI:2387631 Nup42 O Gene nucleoporin 42 10.72 5 24369961 24389011 + AA867018|AB067574|AI426644|AK077066|AK07…
Comment: Rename multiple fastq.gz files
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Jérémie
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Sorry, I misunderstood. Thank you so much for this.
Comment: Integration of transcriptomics and proteomics: difficult matching names
by
sansan_96
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Hello,
This conversion tool has been useful to me, maybe it can help you:
https://biit.cs.ut.ee/gprofiler/convert
Comment: BRAKER3 genome annotation
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sansan_96
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Perhaps eggNOG-MAPPER can be useful for functional annotation:
1. https://academic.oup.com/nar/article/47/D1/D309/5173662
2. http://eggnog…
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Buffo
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I suggest searching for the difference between structural annotation (identifying the coordinates of the ORFs in a sequence) and functional…
Comment: Integration of transcriptomics and proteomics: difficult matchin names
by
ntsopoul
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looks good but I cannot find either Nupl2 nor Nup42 in the list!
Comment: Integration of transcriptomics and proteomics: difficult matchin names
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GenoMax
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This table from Jackson labs that correlates many mouse identifiers with external databases will help. Look at the headers of the columns t…
Comment: Rename multiple fastq.gz files
by
bk11
★
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I just gave hint in the comment above. Please try this, it should work for you.
#!/bin/bash
for file in `ls *fastq.gz`; do
f…
Comment: BRAKER3 genome annotation
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andorjkiss
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I also have this exact same question. I have my entire genome annotated and a braker.GTF file, but without protein "product" names.
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