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News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
5 hours ago by
carlopecoraro2
★ 2.5k
1
vote
2
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1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
10 hours ago by
Zhenyu Zhang
★ 1.2k
0
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115
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News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
2 days ago by
Amos Bairoch
▴ 120
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103
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News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
0
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0
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164
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News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 5 days ago by
Ram
43k • written 5 days ago by
Chakri
• 0
0
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0
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128
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News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 5 days ago by
Ram
43k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
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1
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284
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News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
5 days ago by
David Langenberger
11k
0
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115
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News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
6 days ago by
carlopecoraro2
★ 2.5k
1
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0
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186
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News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
3 days ago by
carlopecoraro2
★ 2.5k
9 results • Page
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Recent Votes
Answer: Association study using SNP data
Comment: agilent human all exon sureselct v7 bed file
Answer: install package
Comment: Overlap File for RACON Genome Polisher
Overlap File for RACON Genome Polisher
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
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Recent Replies
Comment: TaxID mapping file
by
Lada
▴ 30
if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
Answer: install package
by
Pine
▴ 10
To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
Comment: agilent human all exon sureselct v7 bed file
by
MiladAD
▴ 10
God bless you man.
Answer: install package
by
Mathew
▴ 50
Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
by
Lada
▴ 30
thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
by
Jautis
▴ 540
I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
by
drajangirija
• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
bef1
• 0
I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
Comment: Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Expe
by
Mensur Dlakic
★ 27k
Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 50
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 50
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
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