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5 results • Page
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News:
Announcing workshop on Declarative Programming in Biology and Medicine (Seattle, Sept. 2023)
medicine
declmed
declarative
icfp
precision
3 hours ago by
Stephen
• 0
0
votes
0
replies
453
views
News:
Training in Variant Analysis @NIH, January 28-31, 2020
Variant-Calling
next-gen
genome
updated 2 hours ago by
Ram
38k • written 3.3 years ago by
AABI
▴ 130
0
votes
0
replies
14
views
News:
ISMB-affiliated virtual tutorial on Neo4j/Cypher for life sciences
neo4j
cypher
graph
knowledge
1 hour ago by
Stephen
• 0
1
vote
0
replies
782
views
News:
Training in Variant Analysis @NIH, USA, April 16-19,2019
genotype
phenotype
updated 4 hours ago by
Ram
38k • written 4.1 years ago by
AABI
▴ 130
0
votes
0
replies
96
views
News:
course - Reproducibility in Bioinformatics
Docker
Reproducibility
updated 14 minutes ago by
Ram
38k • written 2 days ago by
carlopecoraro2
★ 2.3k
5 results • Page
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Recent Votes
Comment: TSS of protein coding genes
Comment: TSS of protein coding genes
Comment: How to find promoter sequence of a gene?
Answer: BCFtools for somatic vs. germline variant calling
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
Comment: bioinformatics problems solved by graphs data structure
Comment: bioinformatics problems solved by graphs data structure
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Recent Replies
Answer: Make a S4/S3 object with my clinical data
by
ATpoint
70k
Use a SummarizedExperiment. It's assay-agnostic so you can give any assay eith features/genes/observations as rows and samples at columns. …
Comment: TSS of protein coding genes
by
ConvolutedGenome
▴ 10
I seeee Thank you for your input :) !!
Comment: how to get to a VCF from bam files
by
Ram
38k
Read my script - change your bcftools to output VCF, not BCF. File size (as long as it's >0) is not an indicator of anything significant. …
Comment: how to get to a VCF from bam files
by
Human
• 0
Thanks a lot GenoMax and Ram! After a short look into that manual https://samtools.github.io/bcftools/howtos/variant-calling.html I went w…
Answer: BCFtools for somatic vs. germline variant calling
by
Ram
38k
bcftools does not differentiate. It calls variant loci. I don't think there's a single variant caller that calls both germline and somatic …
Comment: What means this Error when running a script in python??
by
Ram
38k
Please format your code properly the next time. I've seen people use wrong formatting options to a reasonable extent, but your formatting w…
Comment: Gaia CNV error TCGA data
by
Ram
38k
1. Don't use people's names as tags. 2. Format your post properly. I've done what I can for now. 3. Add a link to "the tutorial from @kevin…
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
et mon français est assez bien pour comprendre ce que tu as écrit la ;-)
Comment: How to analize multiple letters codes in COG IDs?
by
Constanza
• 0
Thanks for answering so fast, it was very helpful. I shouldn't pay much attention to if COGs are separated by a comma or not then. As long…
Comment: bioinformatics problems solved by graphs data structure
by
lieven.sterck
14k
well, because this is not you guys' private forum, there are other people participating (not native french speaking) , just to give a reaso…
Answer: How to get gene from PSIBLAST resuts
by
lieven.sterck
14k
what you likely will need to do: 1. get the ID of the protein that you are interested in (out of result from PSIBLAST) 2. lookup that ID…
Answer: How to analize multiple letters codes in COG IDs?
by
Mensur Dlakic
★ 23k
The meaning of individual letters is described in a well-known COG functional code: https://ecoliwiki.org/colipedia/index.php/Clusters_o…
Comment: How to find promoter sequence of a gene?
by
sunyeping
▴ 40
The organism is mice.
Answer: How to generate GFF/GTF file from cDNA transcipts FASTA file?
by
Pierre Lindenbaum
153k
BLAT your cDNAs to the reference. This should be a PSL file that can be converted to a psl->gff3 converter (e.g: https://github.com/gperte…
Comment: RNAseq: same reads + more complete scaffold = fewer DEGs?
by
Darked89
4.2k
You may try to check what happened with DEGs obtained using the 300 fragments assembly by getting the sequences of these genes and comparin…
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