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677 results • Page
3 of 14
Sort: Rank
Rank
Views
Votes
Replies
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
2 days ago by
Aspire
▴ 330
1
vote
3
replies
309
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
4 days ago by
Pegasus
▴ 100
0
votes
2
replies
209
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
4 days ago by
Shukai
• 0
1
vote
3
replies
207
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 4 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
mrk
• 0
0
votes
3
replies
250
views
z-score of gene set
z-score
scRNA
gene-set
3 days ago by
Hien
• 0
3
votes
2
replies
215
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 3 days ago by
GenoMax
142k • written 4 days ago by
ashkan
▴ 160
0
votes
0
replies
110
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 4 days ago by
GenoMax
142k • written 4 days ago by
LuciaNhu
• 0
1
vote
2
replies
192
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 4 days ago by
Ram
44k • written 4 days ago by
Harshita
• 0
3
votes
0
replies
121
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 4 days ago by
Ram
44k • written 4 days ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
139
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 4 days ago by
Ram
44k • written 4 days ago by
Fabio Marroni
★ 3.0k
3
votes
5
replies
484
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
4 days ago by
beantkapoor16
▴ 10
0
votes
1
reply
139
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 4 days ago by
DBScan
▴ 310 • written 4 days ago by
brunomiwa
• 0
0
votes
0
replies
93
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
4 days ago by
Ayda Ecem
• 0
0
votes
3
replies
180
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 4 days ago by
Ram
44k • written 4 days ago by
pirku
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 4 days ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
566
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 4 days ago by
Klaus S
▴ 160 • written 6 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
92
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
4 days ago by
Yao
▴ 30
1
vote
1
reply
741
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
19
votes
10
replies
7.4k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
0
votes
0
replies
94
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
4 days ago by
dawnyipingzou
• 0
0
votes
4
replies
245
views
Where to find old version of GATK best practice
gatk
4 days ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
121
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 4 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
Peter Chung
▴ 200
0
votes
0
replies
96
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 4 days ago by
Ram
44k • written 5 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
180
views
CreateSeuratObject taking very long
seurat
2 days ago by
eae6d2e7
• 0
1
vote
2
replies
216
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
5 days ago by
ojaswinipandey
• 0
1
vote
4
replies
317
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 5 days ago by
Ram
44k • written 5 days ago by
Harshita
• 0
2
votes
4
replies
248
views
Filter Genome for Specific Sites
bedtools
updated 5 days ago by
Ram
44k • written 5 days ago by
Anita
• 0
0
votes
3
replies
264
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 5 days ago by
marco.barr
▴ 130 • written 6 days ago by
Mohamed Samir
▴ 30
1
vote
1
reply
134
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 5 days ago by
GenoMax
142k • written 5 days ago by
niruf
• 0
0
votes
0
replies
103
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 5 days ago by
Ram
44k • written 5 days ago by
carlopecoraro2
★ 2.5k
3
votes
0
replies
146
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
5 days ago by
Biostar
2.8k
3
votes
5
replies
451
views
Super ehancers
enhancers
updated 4 days ago by
jared.andrews07
★ 17k • written 23 days ago by
Oburah
• 0
0
votes
2
replies
193
views
vcf phasing
beagle
WhatsHap
phasing
3 days ago by
safeassli
▴ 10
0
votes
2
replies
217
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
5 days ago by
sainavyav22
• 0
0
votes
1
reply
616
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 5 days ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
199
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 5 days ago by
Ram
44k • written 6 days ago by
Sony
▴ 10
0
votes
3
replies
216
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 5 days ago by
Ram
44k • written 5 days ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
103
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 5 days ago by
Ram
44k • written 5 days ago by
ev97
▴ 20
0
votes
1
reply
147
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 5 days ago by
marco.barr
▴ 130 • written 5 days ago by
sooni
▴ 20
0
votes
1
reply
115
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 5 days ago by
GenoMax
142k • written 5 days ago by
jinyi
• 0
0
votes
0
replies
181
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 5 days ago by
Ram
44k • written 5 days ago by
JorgeVallejo
▴ 20
0
votes
0
replies
107
views
transcriptome annotation
annotation
trinity
transcriptome
updated 5 days ago by
Ram
44k • written 5 days ago by
Asim Bin Arshad
• 0
0
votes
5
replies
247
views
Why most genes have high padj values
RNA-seq
DEG
updated 5 days ago by
Ram
44k • written 5 days ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 6 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
157
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 5 days ago by
zx8754
11k • written 6 days ago by
Ali
• 0
0
votes
4
replies
267
views
GO analysis: p-value range
GO
R
updated 5 days ago by
Matthias Zepper
4.6k • written 6 days ago by
sooni
▴ 20
1
vote
2
replies
244
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 4 days ago by
colindaven
6.4k • written 6 days ago by
Dr.
• 0
1
vote
3
replies
259
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 5 days ago by
GenoMax
142k • written 7 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
107
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
6 days ago by
Maryam
• 0
0
votes
4
replies
359
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
6 days ago by
Bibi
• 0
677 results • Page
3 of 14
Recent Votes
Low DESeq2 Sensivity on scRNA Pseudobulk Samples
DESEQ2: How can I convert ensembl gene id's to HGNC gene names.
Problem with Ensembl version identifiers after running DESeq2
Issues with adding gene name and entrez ID to DESeq2 result having Ensembl ID.
A: Looking for differential gene expression between treatment, within a specific cl
How to compare cell-type ratios in sc-RNA seq data?
How to calculate cell type frequency between two groups in single cell data
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Recent Replies
Comment: Merging multiple samples in Seurat
by
Picasa
▴ 640
did you split by sample or donor ?
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
For downstream analysis, after integration, my plan is to annotate each cluster/cell type and then perform a DGE analysis of KO versus WT f…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
That is correct
Answer: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
ATpoint
82k
That depends on the data and the marker. Generally I would plot violins per cluster for the marker(s) and see whether one robustly overexpr…
Comment: Error when i use EVidenceModeler to do the genome annotation
by
peanut
• 0
thank you so much ,i get it
Comment: Number of non-ATCG nucleotides replaced by Salmon
by
Tonya S.
▴ 10
Oops, yes, that must be where they are coming from. For some reason, I was thinking the genome was just soft-masked. How embarrassing! Than…
Answer: Number of non-ATCG nucleotides replaced by Salmon
by
Rob
6.6k
If there are no other signs that anything is awry, I probably wouldn't worry about this. Is it possible that these non-canonical nucleotid…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
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