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Answer: Piping samtools to R
Answer: How to filter columns in a raw sparse matrix in R
Convert GFF3 to splice junction BED file, for filtering variants multi-sample (RNA-seq) VCF
Answer: Convert GFF3 to splice junction BED file, for filtering variants multi-sample (
Answer: How to filter columns in a raw sparse matrix in R
Comment: Integration of transcriptomics and proteomics: difficult matching names
Comment: Integration of transcriptomics and proteomics: difficult matching names
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Recent Replies
Comment: Can I compare kallisto counts from samples with different amount of reads?
by
bioinfo
▴ 150
Thank you. I ended up using seqtk to downsample the data.
Answer: Piping samtools to R
by
joe
▴ 490
This is straightforward. Can perform functions on multiple lines at a time if they are loaded as such. Skeleton script below; func.1…
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
by
Ram
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You should **at least** include links to the other post in each post to make users aware that you're seeking help in multiple places.
Comment: Rename multiple fastq.gz files
by
shenwei356
8.4k
Here's another safe solution using [brename](https://www.biostars.org/p/9487877/) ([download](https://github.com/shenwei356/brename/release…
Comment: How to filter columns in a raw sparse matrix in R
by
bgbs
• 0
Hi, it worked, thank you so much!
Comment: Prediction tools summary - zero values
by
Дана
• 0
Hello, Lucas. Would you be so kind to share the link or id of your Schizophrenia vcf dataset? I am a student in masters degree and I am int…
Comment: GSEA analysis in R
by
sansan_96
▴ 80
One example: ``` ### ego3 <- gseGO(geneList = geneList, OrgDb = org.Hs.eg.db, ont = "CC", …
Answer: 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
by
ntsopoul
▴ 60
you are right! Excel just did not find it...
Answer: Integration of transcriptomics and proteomics: difficult matching names
by
ntsopoul
▴ 60
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
by
Koketso
• 0
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
by
ATpoint
81k
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: Rename multiple fastq.gz files
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bk11
★ 2.3k
Of course! If it worked, accept the answer.
Comment: Integration of transcriptomics and proteomics: difficult matching names
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GenoMax
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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
• 0
Sorry, I misunderstood. Thank you so much for this.
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