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176 results • Page
4 of 4
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0
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70
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Herald:
The Biostar Herald for Monday, May 06, 2024
herald
11 hours ago by
Biostar
2.7k
0
votes
0
replies
53
views
vdjtools
vdjtools
10 hours ago by
yueli7
▴ 250
0
votes
0
replies
45
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
9 hours ago by
Javier
• 0
0
votes
0
replies
53
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
9 hours ago by
MAPK2
▴ 40
0
votes
0
replies
52
views
Cox Model with interaction item interpretation
Cox
9 hours ago by
Bine
▴ 60
0
votes
0
replies
124
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 5 days ago by
Ram
43k • written 5 days ago by
Oscar
▴ 10
0
votes
0
replies
134
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
6 days ago by
Bine
▴ 60
0
votes
0
replies
98
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
5 days ago by
meck
• 0
0
votes
0
replies
116
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
6 days ago by
fanglujing
▴ 60
0
votes
0
replies
106
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
5 days ago by
VITALA
• 0
0
votes
0
replies
145
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
6 days ago by
O.rka
▴ 710
0
votes
0
replies
164
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 6 days ago by
Ram
43k • written 6 days ago by
Chakri
• 0
0
votes
0
replies
126
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 6 days ago by
Ram
43k • written 6 days ago by
Alexandros
• 0
0
votes
0
replies
57
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
2 hours ago by
Guillermo
• 0
0
votes
0
replies
11
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
42 minutes ago by
heelpPlease
• 0
0
votes
0
replies
45
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
4 hours ago by
belloy
• 0
0
votes
0
replies
132
views
Homer motif analysis
Homer
2 days ago by
daffodil
▴ 10
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
3 days ago by
Chris
▴ 260
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
1 day ago by
Ibrahim Tanyalcin
★ 1.2k
0
votes
0
replies
100
views
Seurat V5 integration
Seurat
samples
integration
combine
1 day ago by
starswillfade
▴ 10
0
votes
0
replies
97
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
1 day ago by
DGTool
• 0
0
votes
0
replies
84
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
38
views
Cellphonedb results
cpdb
visulization
cellphonedb
4 hours ago by
piotto
▴ 20
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
3 days ago by
Javier
• 0
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
3 days ago by
mikemakaveli1
• 0
0
votes
0
replies
89
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
1 day ago by
Christopher
• 0
176 results • Page
4 of 4
Recent Votes
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
Answer: Gene ontology and homologs
Comment: anRichment is missing
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Recent Awards •
All
Popular Question
to
Scott McKay
▴ 30
Popular Question
to
A. Domingues
★ 2.7k
Scholar
to
LChart
3.9k
Popular Question
to
JACKY
▴ 140
Popular Question
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bhumm
▴ 140
Teacher
to
Matthias Zepper
4.6k
Popular Question
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sidrah.maryam
▴ 50
Recent Replies
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom
by
LChart
3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file?
by
GenoMax
142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file?
by
LChart
3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
• 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
by
dsull
★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
by
GenoMax
142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
• 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
by
GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
by
Tatyana
• 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
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