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116,890 results • Page
3 of 2338
Sort: Rank
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0
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90
views
Blog:
Overview of Nanopore Sequencing
biotech
5 days ago by
usa.cd.genomics
• 0
0
votes
0
replies
102
views
meffil.snp.concordance
meffil
methylation
snp_concordance
5 days ago by
kyj222637
• 0
0
votes
1
reply
146
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 4 days ago by
Bastien Hervé
5.3k • written 5 days ago by
sooni
▴ 20
1
vote
5
replies
415
views
HCL database download
HCL
updated 5 days ago by
Ram
43k • written 9 days ago by
sooni
▴ 20
0
votes
1
reply
246
views
barcode of TCR-sequencing
barcode
updated 5 days ago by
mizraelson
▴ 60 • written 12 days ago by
yueli7
▴ 250
0
votes
3
replies
228
views
STAR aligner error
RNA-seq
STAR
slurm
updated 4 days ago by
Ram
43k • written 5 days ago by
M.
▴ 30
0
votes
0
replies
96
views
monocle 3-- Could not get node in small cluster
monocle3
5 days ago by
synat.keam
▴ 100
0
votes
2
replies
195
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
4 days ago by
Nicholas
• 0
1
vote
4
replies
365
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
5 days ago by
heelpPlease
• 0
0
votes
7
replies
478
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 4 days ago by
Wayne
★ 2.0k • written 6 days ago by
JACKY
▴ 140
0
votes
0
replies
111
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
466
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 5 days ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
244
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Sony
▴ 10
5
votes
5
replies
282
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
5 days ago by
Chris
▴ 280
0
votes
2
replies
211
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
349
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 2 days ago by
i.sudbery
19k • written 5 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
163
views
student
epitranscriptomics
updated 5 days ago by
ATpoint
82k • written 5 days ago by
useriwa
• 0
0
votes
0
replies
108
views
Imputation of missing genotypes
panel
beagle
imputation
5 days ago by
analyst
▴ 50
0
votes
3
replies
170
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Assa Yeroslaviz
★ 1.8k
7
votes
1
reply
166
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 5 days ago by
dariober
14k • written 5 days ago by
nhaus
▴ 360
2
votes
2
replies
172
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
5 days ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
260
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 5 days ago by
Weiwen
• 0 • written 6 days ago by
MICOS
▴ 10
0
votes
4
replies
268
views
Correlation Analysis
statistics
methylation
NGS
expression
1 day ago by
Researcher
▴ 30
1
vote
2
replies
176
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
5 days ago by
robert.flynn.21
• 0
1
vote
1
reply
217
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 5 days ago by
Michael
54k • written 6 days ago by
Guillermo
• 0
1
vote
5
replies
339
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 4 days ago by
Michael
54k • written 5 days ago by
qwertyuiop26
• 0
0
votes
1
reply
177
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 6 days ago by
ATpoint
82k • written 6 days ago by
MAPK2
▴ 40
0
votes
2
replies
252
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 6 days ago by
Xiaofen
• 0 • written 6 days ago by
toddknutson
▴ 60
0
votes
1
reply
132
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 6 days ago by
LChart
3.9k • written 6 days ago by
David
• 0
2
votes
2
replies
179
views
Where to get the following bed file?
WES
bed
reference
file
updated 6 days ago by
GenoMax
142k • written 6 days ago by
wyuan37
• 0
0
votes
0
replies
114
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
6 days ago by
Scott McKay
▴ 30
0
votes
0
replies
106
views
Cellphonedb results
cpdb
visulization
cellphonedb
6 days ago by
piotto
▴ 20
0
votes
0
replies
137
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
6 days ago by
belloy
• 0
1
vote
3
replies
254
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 6 days ago by
swbarnes2
14k • written 6 days ago by
Ngrin
• 0
1
vote
6
replies
695
views
anRichment is missing
WGCNA
anRichment
updated 6 days ago by
GenoMax
142k • written 6 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
206
views
Gene ontology and homologs
gene-ontology
updated 6 days ago by
geneontologyhelp
▴ 400 • written 7 days ago by
beshka194
• 0
1
vote
2
replies
237
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 6 days ago by
zx8754
11k • written 6 days ago by
snajafy
• 0
0
votes
0
replies
114
views
Cox Model with interaction item interpretation
Cox
6 days ago by
Bine
▴ 60
0
votes
0
replies
100
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
3 days ago by
Javier
• 0
1
vote
7
replies
495
views
Question regarding WGCNA
WGCNA
Network-construction
3 days ago by
deepak
• 0
0
votes
0
replies
107
views
vdjtools
vdjtools
6 days ago by
yueli7
▴ 250
1
vote
0
replies
148
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
6 days ago by
Biostar
2.7k
0
votes
1
reply
287
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 5 days ago by
andres.firrincieli
3.6k • written 6 days ago by
Antonio
• 0
0
votes
0
replies
117
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 6 days ago by
Ram
43k • written 6 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
102
views
Normalizing AMR gene count data
abundance
RGI
updated 6 days ago by
Ram
43k • written 6 days ago by
arshad1292
▴ 100
1
vote
0
replies
132
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
sarumonsus
▴ 10
0
votes
0
replies
121
views
How to implement an IGV to streamlit app?
python
streamlit
igv
6 days ago by
avigail.shnaider
• 0
1
vote
5
replies
325
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 6 days ago by
Ram
43k • written 7 days ago by
snajafy
• 0
0
votes
2
replies
275
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 6 days ago by
GenoMax
142k • written 7 days ago by
mropri
▴ 150
0
votes
1
reply
302
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 7 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
116,890 results • Page
3 of 2338
Recent Votes
A: How to integrate multiple data sets from microarray platform prior meta-analysis
How to integrate multiple data sets from microarray platform prior meta-analysis?
A: NCBI Accession Number to Taxonomy ID
Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
Comment: automatic clustering annotation using python
automatic clustering annotation using python
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rj.rezwan
• 0
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colindaven
6.4k
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pjb39
▴ 200
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Comment: java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
by
analyst
▴ 50
# COMMAND FOR BQSR # step 1: building the model java -jar -Xmx50G gatk.jar BaseRecalibrator -I input.bam -R whaet.fa --known-sites w…
Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
While running with this batch option batch --method wgs option. I have used this command " cnvkit.py batch tumor.bam -n normal.bam -m wgs -…
Answer: Generating .bed file and .map file for polyploid vcf file through plink
by
chrchang523
10k
Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
Comment: Extracting mutation status from MAF files - TCGA
by
Zhenyu Zhang
★ 1.2k
you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
Comment: Obtaining Infinium Methylation450K manifest for hg38
by
Zhenyu Zhang
★ 1.2k
Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
Answer: Nomalization - TCGA, RNA-seq and Microarray
by
Zhenyu Zhang
★ 1.2k
You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
by
ATpoint
82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
Comment: Longest transcript variant per gene
by
sansan_96
▴ 90
Thank you very much, success in your projects.
Comment: In IGV is this a heterogeneous mutation or false call?
by
Tuck898
• 0
Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Pine
▴ 20
This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
▴ 40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
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