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116,787 results • Page
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0
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Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 1 hour ago by
LChart
3.9k • written 2 hours ago by
David
• 0
0
votes
1
reply
22
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
updated 40 minutes ago by
GenoMax
142k • written 1 hour ago by
heelpPlease
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
1
vote
2
replies
69
views
Where to get the following bed file?
WES
bed
reference
file
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
wyuan37
• 0
0
votes
0
replies
66
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
3 hours ago by
Guillermo
• 0
0
votes
0
replies
40
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
5 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
39
views
Cellphonedb results
cpdb
visulization
cellphonedb
5 hours ago by
piotto
▴ 20
0
votes
0
replies
46
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
5 hours ago by
belloy
• 0
0
votes
2
replies
101
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
5 hours ago by
Ngrin
• 0
0
votes
1
reply
85
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
updated 5 hours ago by
Wayne
★ 2.0k • written 7 hours ago by
JACKY
▴ 140
1
vote
6
replies
591
views
anRichment is missing
WGCNA
anRichment
updated 7 hours ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
139
views
Gene ontology and homologs
gene-ontology
updated 9 hours ago by
geneontologyhelp
▴ 400 • written 1 day ago by
beshka194
• 0
1
vote
2
replies
152
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 6 hours ago by
zx8754
11k • written 14 hours ago by
snajafy
• 0
0
votes
0
replies
53
views
Cox Model with interaction item interpretation
Cox
10 hours ago by
Bine
▴ 60
0
votes
0
replies
54
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
10 hours ago by
MAPK2
▴ 40
0
votes
0
replies
47
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
10 hours ago by
Javier
• 0
0
votes
4
replies
303
views
Question regarding WGCNA
WGCNA
Network-construction
updated 8 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
56
views
vdjtools
vdjtools
11 hours ago by
yueli7
▴ 250
0
votes
0
replies
72
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
12 hours ago by
Biostar
2.7k
0
votes
1
reply
94
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 8 hours ago by
andres.firrincieli
3.6k • written 13 hours ago by
Antonio
• 0
0
votes
0
replies
65
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 13 hours ago by
Ram
43k • written 13 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
52
views
Normalizing AMR gene count data
abundance
RGI
updated 13 hours ago by
Ram
43k • written 13 hours ago by
arshad1292
▴ 100
0
votes
0
replies
75
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 13 hours ago by
Ram
43k • written 15 hours ago by
MICOS
• 0
0
votes
0
replies
64
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 16 hours ago by
Pierre Lindenbaum
161k • written 16 hours ago by
sarumonsus
• 0
0
votes
2
replies
243
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
6 hours ago by
M.
▴ 30
0
votes
0
replies
75
views
How to implement an IGV to streamlit app?
python
streamlit
igv
17 hours ago by
avigail.shnaider
• 0
1
vote
5
replies
250
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 13 hours ago by
Ram
43k • written 19 hours ago by
snajafy
• 0
0
votes
2
replies
170
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 13 hours ago by
GenoMax
142k • written 1 day ago by
mropri
▴ 150
0
votes
1
reply
269
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 1 day ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
2
votes
2
replies
194
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
1 day ago by
brandon
• 0
0
votes
0
replies
92
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
1 day ago by
KHURRAM SHAHZAD
• 0
1
vote
5
replies
320
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 12 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
0
replies
91
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
1 day ago by
Christopher
• 0
4
votes
1
reply
199
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 17 hours ago by
zx8754
11k • written 2 days ago by
Jautis
▴ 560
2
votes
2
replies
285
views
Association study using SNP data
Association
Allele
Parentage
SNP
1 day ago by
drajangirija
• 0
0
votes
0
replies
85
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
98
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
1 day ago by
DGTool
• 0
0
votes
0
replies
101
views
Seurat V5 integration
Seurat
samples
integration
combine
1 day ago by
starswillfade
▴ 10
0
votes
1
reply
140
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 5 hours ago by
bk11
★ 2.4k • written 1 day ago by
Yoosef
▴ 60
0
votes
1
reply
371
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 1 day ago by
GenoMax
142k • written 1 day ago by
tulip
• 0
3
votes
4
replies
376
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 4 hours ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
SHN
▴ 40
4
votes
2
replies
228
views
GRCh38.gmap file
gnomix
gmap
2 days ago by
lorena9132
▴ 10
2
votes
3
replies
797
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 2 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
238
views
creating batch colum for batch correction
batch-correction
combat
15 hours ago by
Expert
▴ 10
1
vote
4
replies
322
views
Segmentation error while using a tool
smalt
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Ruqaiya
• 0
0
votes
1
reply
188
views
Help with DGEList function
DGEList
R
updated 1 day ago by
marco.barr
▴ 90 • written 2 days ago by
Natali
• 0
0
votes
0
replies
133
views
Homer motif analysis
Homer
2 days ago by
daffodil
▴ 10
0
votes
1
reply
172
views
HCL database download
database
HCL
human
updated 2 days ago by
GenoMax
142k • written 2 days ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
1 day ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
288
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 3 days ago by
chrchang523
10k • written 6 days ago by
8armed
▴ 10
116,787 results • Page
1 of 2336
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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Scott McKay
▴ 30
Popular Question
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A. Domingues
★ 2.7k
Scholar
to
LChart
3.9k
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▴ 140
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Recent Replies
Comment: Understanding STAR output (Aligned.out.sam file)
by
GenoMax
142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
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…
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