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125 results • Page
3 of 3
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25
views
Request for Bioinformatics Workstation Configuration for Bacterial Whole Genome Analysis?
Bacterial
Workstation
Whole
genome
AMR
1 hour ago by
mathavanbioinfo
▴ 80
0
votes
0
replies
146
views
How to combine replicates in profile plot in profileplyr package?
ATAC-Seq
profilePlot
profilePlyr
updated 2 days ago by
GenoMax
147k • written 3 days ago by
B.N.
▴ 10
0
votes
0
replies
213
views
Homer annotatePeaks.pl output
start
annotatePeaks.pl
chr
homer
position
updated 5 days ago by
GenoMax
147k • written 5 days ago by
Rakesh
• 0
0
votes
0
replies
109
views
Should we normalize/transform WGBS beta values?
normalization
WGBS
methylation
transfromation
2 days ago by
Lalaland
▴ 40
1
vote
0
replies
278
views
is there any data base or reference to provide a comprehensive list of CD marker expression in different white blood cell types?
DEG
myeloid
CDmarker
leukocyte
2 days ago by
qasemi.m.q
▴ 10
0
votes
0
replies
102
views
Intersect between bedGraph and bed file
count
bedtools
bedGraph
Matrix
1 day ago by
daffodil
▴ 10
0
votes
0
replies
87
views
News:
Master Evidence Synthesis with Meta-analysis in R (Online Course - Feb 10-14, 2025)
Meta-analysis
Review
Evidence-Synthesis
1 day ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
182
views
Job:
Postdoc in reproductive genetics, University of Gothenburg, Sweden
bioinformatics
computational-biology
genetics
postdoc
updated 6 days ago by
Ram
44k • written 7 days ago by
pol.sole.navais
• 0
0
votes
0
replies
217
views
Signac for mgatk scRNA-seq data
mgatk
Signac
scRNA-seq
5 days ago by
marco.barr
▴ 150
0
votes
0
replies
210
views
Is there a function in cytoscape for calculating node strength ?
network
cytoscape
igraph
5 days ago by
SplitInf
▴ 10
0
votes
0
replies
86
views
Packages for constructing Phylogenetic tree from HapMap file
HapMap
tree
Phylogenetic
SNP
1 day ago by
sujee119
• 0
0
votes
0
replies
15
views
Overlap entries in annotation
Bedtools
28 minutes ago by
Muhammad
• 0
0
votes
0
replies
167
views
split gamp by chromosome or extract specific regions.
vg
6 days ago by
Juhyun
• 0
0
votes
0
replies
202
views
GEOquery getGEO is normalized data or not?
getgeo
geoquery
microarray
5 days ago by
tyasird
▴ 10
0
votes
0
replies
71
views
Blog:
Tools and Future of eQTL: Data Gathering and Application in Genetic Medicine
eQTL
SNPs
GWAS
1 day ago by
Novogene
▴ 460
0
votes
0
replies
72
views
Mapping gene symbols to MONDO codes
mondo
genes
mapping
1 day ago by
CRivi
• 0
0
votes
0
replies
92
views
Germline CNV CALLING
gErmline
CNV
updated 22 hours ago by
GenoMax
147k • written 1 day ago by
Smilesky
• 0
0
votes
0
replies
102
views
Herald:
The Biostar Herald for Monday, November 11, 2024
herald
21 hours ago by
Biostar
3.0k
0
votes
0
replies
166
views
Phasing haplotypes from the crosses
gatk
snps
phasing
haplotypes
6 days ago by
ayeraselvan
▴ 10
0
votes
0
replies
221
views
EU-Seq Differentially expressed transcripts
EU-Seq
Seq
nascent
RNA
6 days ago by
Bruno
• 0
0
votes
0
replies
12
views
Somatic-Sniper calls very few variants
sniper
somatic
18 minutes ago by
runfreely2
• 0
0
votes
0
replies
230
views
Job:
Seeking remote internship/job
spain
remote
europe
portugal
6 days ago by
Guilherme
• 0
0
votes
0
replies
52
views
Manta crash during getDepthFromAlignments
manta
sv
updated 12 hours ago by
GenoMax
147k • written 12 hours ago by
lucas.lochovsky
• 0
0
votes
0
replies
3
views
Currently recommended Oxford Nanopore data basecalling and preprocessing pipeline for de novo assembly applications
ONT
assembly
Nanopore
preprocessing
basecalling
just now by
Denis
▴ 310
0
votes
0
replies
55
views
Error: No sites have activity greater than filter value.
diffbind
8 hours ago by
kim
• 0
125 results • Page
3 of 3
Recent Votes
Comment: R studio
Comment: Assigning taxonomic features in CAT: incorrect species annotation?
Comment: How to interpret ANCOM-BC results when diff is true but passed_ss is false?
Answer: Where can I download a BED file with exonic regions?
Comment: Merge braker.gtf and SQANT3.gff3 file
Comment: Which Phred value to use in trimming
Answer: Downloading synonyms for dbSNP rsids
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Recent Awards •
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Popular Question
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Denis
▴ 310
Popular Question
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mathavanbioinfo
▴ 80
Popular Question
to
QX
▴ 60
Scholar
to
ATpoint
85k
Popular Question
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Sakura
• 0
Popular Question
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lucas.lochovsky
• 0
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Mitchell.frederick
▴ 10
Recent Replies
Comment: Batch correction
by
ATpoint
85k
I would first of all run the most old-fashioned and robust approach there is: Normalize data with edgeR to get logCPMs, run `removeBatchEff…
Comment: Assigning taxonomic features in CAT: incorrect species annotation?
by
DriesB
▴ 110
> Also, if we assume that ORF4 and ORF5 are from different species, shouldn't their annotation then be copied to genus and family rank? Wi…
Comment: Assigning taxonomic features in CAT: incorrect species annotation?
by
DriesB
▴ 110
Thank you for replying. However, isn't this mostly rephrasing the question, instead of answering it?
Comment: Assigning taxonomic features in CAT: incorrect species annotation?
by
DriesB
▴ 110
(I think it could probably be changed to an answer, instead of a comment)
Comment: Assigning taxonomic features in CAT: incorrect species annotation?
by
DriesB
▴ 110
Thank you for the resolute reply!
Comment: Batch correction
by
Sakura
• 0
Thanks for your reply. In the local data, we have data for disease group (1) vs. control disease, and in the public data, we have data f…
Comment: Batch correction
by
ATpoint
85k
Can you show an overview which groups are in your data and which groups are in the public data? If your data are nested, meaning like all c…
Comment: How to interpret ANCOM-BC results when diff is true but passed_ss is false?
by
andres.firrincieli
3.8k
columns with the term `intercept` can be ignored in ancombc. Have alook at the github page: https://github.com/FrederickHuangLin/ANCOMBC
Comment: Merge braker.gtf and SQANT3.gff3 file
by
anna_shin
• 0
thank you. I will try using AGAT toolkit.
Answer: HOMER annotateInteractions.pl error
by
JJJelly
• 0
i had same error. Please let me know how to solve this problem
Answer: TCGA Methylation Beta and Gene Expression Help
by
Zhenyu Zhang
★ 1.2k
1. yes, you got why there are multiple genes 2. if you downloaded the data from the GDC, here is the reference file page https://gdc.cance…
Answer: Converting ICGC ids to TCGA format
by
Zhenyu Zhang
★ 1.2k
The aliquot_ids and submitter_ids seem to be cghub ids
Answer: merge my own RNA-seq data with TCGA UCSCXena data sets. and proper normalisatio
by
Zhenyu Zhang
★ 1.2k
For a careful analysis, how about you download data from the GDC, and run your samples via the GDC RNA-Seq pipeline. Then you can use the s…
Answer: How to get full list of TCGA patients with mutation data
by
Zhenyu Zhang
★ 1.2k
Go to GDC Cohort Builder, filter for TCGA and MAF
Comment: NCI Genomic Data Commons gdc-rnaseq-tool
by
Zhenyu Zhang
★ 1.2k
This tool was developed 5 years ago. GDC has changed RNA-Seq quantification file format 2.5 years ago during Gencode v36 update
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