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13,535 results • Page
1 of 271
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0
votes
1
reply
74
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 25 minutes ago by
ATpoint
82k • written 16 hours ago by
MAPK2
▴ 40
0
votes
1
reply
69
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 3 hours ago by
Xiaofen
• 0 • written 5 hours ago by
toddknutson
▴ 60
0
votes
1
reply
67
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 7 hours ago by
LChart
3.9k • written 8 hours ago by
David
• 0
0
votes
2
replies
89
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
updated 40 minutes ago by
swbarnes2
14k • written 7 hours 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
99
views
Where to get the following bed file?
WES
bed
reference
file
updated 10 hours ago by
GenoMax
142k • written 10 hours ago by
wyuan37
• 0
0
votes
0
replies
83
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
9 hours ago by
Guillermo
• 0
0
votes
0
replies
54
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
10 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
54
views
Cellphonedb results
cpdb
visulization
cellphonedb
10 hours ago by
piotto
▴ 20
0
votes
0
replies
64
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
11 hours ago by
belloy
• 0
0
votes
3
replies
133
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 41 minutes ago by
swbarnes2
14k • written 12 hours ago by
Ngrin
• 0
0
votes
1
reply
109
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
updated 11 hours ago by
Wayne
★ 2.0k • written 13 hours ago by
JACKY
▴ 140
1
vote
6
replies
625
views
anRichment is missing
WGCNA
anRichment
updated 13 hours ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
156
views
Gene ontology and homologs
gene-ontology
updated 14 hours ago by
geneontologyhelp
▴ 400 • written 1 day ago by
beshka194
• 0
1
vote
2
replies
167
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 12 hours ago by
zx8754
11k • written 20 hours ago by
snajafy
• 0
0
votes
0
replies
66
views
Cox Model with interaction item interpretation
Cox
16 hours ago by
Bine
▴ 60
0
votes
0
replies
58
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
16 hours ago by
Javier
• 0
0
votes
4
replies
313
views
Question regarding WGCNA
WGCNA
Network-construction
updated 14 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
67
views
vdjtools
vdjtools
17 hours ago by
yueli7
▴ 250
0
votes
0
replies
88
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
17 hours ago by
Biostar
2.7k
0
votes
1
reply
109
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 14 hours ago by
andres.firrincieli
3.6k • written 18 hours ago by
Antonio
• 0
0
votes
0
replies
78
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 19 hours ago by
Ram
43k • written 19 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
65
views
Normalizing AMR gene count data
abundance
RGI
updated 19 hours ago by
Ram
43k • written 19 hours ago by
arshad1292
▴ 100
0
votes
1
reply
114
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
4 hours ago by
MICOS
• 0
0
votes
0
replies
76
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 22 hours ago by
Pierre Lindenbaum
161k • written 22 hours ago by
sarumonsus
• 0
0
votes
2
replies
252
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
12 hours ago by
M.
▴ 30
0
votes
0
replies
86
views
How to implement an IGV to streamlit app?
python
streamlit
igv
23 hours ago by
avigail.shnaider
• 0
1
vote
5
replies
260
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 19 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
2
replies
183
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 19 hours ago by
GenoMax
142k • written 1 day ago by
mropri
▴ 150
0
votes
1
reply
277
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
204
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
101
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
1 day ago by
KHURRAM SHAHZAD
• 0
1
vote
5
replies
331
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 18 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
0
replies
98
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
209
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 23 hours ago by
zx8754
11k • written 2 days ago by
Jautis
▴ 560
2
votes
2
replies
295
views
Association study using SNP data
Association
Allele
Parentage
SNP
1 day ago by
drajangirija
• 0
0
votes
0
replies
92
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
105
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
1 day ago by
DGTool
• 0
0
votes
0
replies
111
views
Seurat V5 integration
Seurat
samples
integration
combine
1 day ago by
starswillfade
▴ 10
0
votes
1
reply
161
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 11 hours ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
0
votes
1
reply
413
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 2 days ago by
tulip
• 0
3
votes
4
replies
392
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 9 hours ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
SHN
▴ 40
4
votes
2
replies
239
views
GRCh38.gmap file
gnomix
gmap
2 days ago by
lorena9132
▴ 10
2
votes
3
replies
807
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
248
views
creating batch colum for batch correction
batch-correction
combat
21 hours ago by
Expert
▴ 10
1
vote
4
replies
332
views
Segmentation error while using a tool
smalt
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
198
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
141
views
Homer motif analysis
Homer
2 days ago by
daffodil
▴ 10
0
votes
3
replies
221
views
HCL database download
database
HCL
human
1 hour ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
2 days ago by
Zhenyu Zhang
★ 1.2k
13,535 results • Page
1 of 271
Recent Votes
Comment: Gene Specific coverage from WGS data
Answer: ATAC-Seq and RPKM
Answer: MSA and distance matrix in R
Comment: MSA and distance matrix in R
Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
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Recent Replies
Answer: What is the proper way to identify the cell types of scRNAseq cluster?
by
ATpoint
82k
I will say that the proper way is the one that confidently identifies your celltypes. > optimal number of marker genes to consider. T…
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
swbarnes2
14k
When everything is the same size, correcting for size is pointless. It doesn't change the numbers much at all.
Comment: Understanding STAR output (Aligned.out.sam file)
by
swbarnes2
14k
What do the alignments look like in IGV?
Comment: HCL database download
by
sooni
▴ 20
I solved the problem! Thanks!
Comment: Gene Specific coverage from WGS data
by
Adyasha
• 0
Thank you, here I am giving you some example , suppose I have bam files . 1.bam 2.bam 3.bam 4.bam now I want to see Spike gene coverage in …
Answer: Bioinformatics Analyst - Laboratory Medicine and Pathology
by
Xiaofen
• 0
I'm having a problem and I can't find the button to post, how do you post?
Comment: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
by
MICOS
• 0
Contest question details: **To effectively address the accuracy and efficiency issues of clustering algorithms used for spatial transcript…
Comment: HCL database download
by
sooni
▴ 20
I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
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?
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