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679 results • Page 1 of 14
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45
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat Pseudobulk single-cell DESeq2 scRNA analysis
6 hours ago by Sara ▴ 30
0
votes
0
replies
59
views
How to decrease the motif score?
scores Motif
11 hours ago by Hadia • 0
0
votes
0
replies
54
views
immuCell Abundance infiltrate
ImmuCell Abundance infiltrate
updated 11 hours ago by 162k • written 11 hours ago by • 0
0
votes
1
reply
101
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 14 hours ago by 82k • written 17 hours ago by ▴ 40
0
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0
replies
53
views
MaxEntScan for rMATS results
MaxEntScan rMATS
15 hours ago by adi.gershon1 • 0
0
votes
0
replies
116
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ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker. MAKER. annotation.
21 hours ago by Sony ▴ 10
0
votes
0
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70
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK GWAS SNP
22 hours ago by F110152169 • 0
4
votes
2
replies
152
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq stringtie indexing salmon
updated 23 hours ago by 6.6k • written 23 hours ago by ▴ 10
0
votes
3
replies
244
views
Tool: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux NovaSeq Illumina Demultiplexing Barcode
1 day ago by Brian Bushnell 20k
2
votes
10
replies
649
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r ComplexHeatmap
1 day ago by hannes.bongartz • 0
0
votes
0
replies
88
views
perl Error - needLargeMem Bigwig
Bigwig perl mitosalt
1 day ago by marco.barr ▴ 130
0
votes
0
replies
84
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
1 day ago by niconps14 • 0
0
votes
3
replies
217
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 1 day ago by 162k • written 1 day ago by • 0
2
votes
4
replies
252
views
Harmony integration group.by.var parameter
single-cell harmony
13 hours ago by Picasa ▴ 640
2
votes
1
reply
132
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF gnomAD SNP
updated 1 day ago by 22k • written 1 day ago by ▴ 10
0
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0
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79
views
Exon Annotation failed using homer annotatePeaks.pl
homer alternative-splicing annotatePeaks
updated 1 day ago by 44k • written 1 day ago by • 0
1
vote
3
replies
213
views
How to calculate cell type frequency between two groups in single cell data
Seurat single-cell sc-RNA cell-type
updated 13 hours ago by 5.3k • written 1 day ago by ▴ 30
0
votes
1
reply
123
views
Mutation counts corrected by number of samples
mutations WES genomics WGS
updated 1 day ago by 44k • written 1 day ago by ▴ 50
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 1 day ago by 44k • written 3.6 years ago by • 0
0
votes
1
reply
344
views
LDhat lookup table
LDhat
updated 1 day ago by 44k • written 11 months ago by ▴ 10
0
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0
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93
views
BAM to Bedgraph creating an empty file
Bisulfite-seq bismark
1 day ago by irebekah.c • 0
0
votes
0
replies
88
views
Can you use a polygenic risk score for a trait (e.g., BMI) in association analyses when it doesn't associate with BMI in the sample it is used?
polygenic-risk-score imputation
updated 1 day ago by 44k • written 1 day ago by ▴ 10
0
votes
5
replies
203
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
1 day ago by Deepthi • 0
0
votes
1
reply
202
views
Annotating single cell data automatically
single-cell
updated 1 day ago by 44k • written 4 weeks ago by • 0
1
vote
4
replies
258
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
1 day ago by sc_analysis • 0
0
votes
1
reply
152
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat scRNA-seq UMAP
updated 1 day ago by 5.3k • written 1 day ago by ▴ 10
3
votes
4
replies
430
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 1 day ago by ★ 1.7k • written 9 days ago by ▴ 130
0
votes
0
replies
113
views
R code for KEGG pathways output
KEGGREST dplyr KEGG R
1 day ago by doramora ▴ 10
0
votes
0
replies
86
views
finding highly divergent orthologs using exonerate
ortholog Exonerate evolution
1 day ago by Emily ▴ 20
2
votes
3
replies
211
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity mtDNA PacBio
1 day ago by hashim.rana11 ▴ 20
0
votes
1
reply
140
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 1 day ago by 162k • written 1 day ago by • 0
1
vote
2
replies
226
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK GWAS SNP
1 day ago by F110152169 • 0
8
votes
9
replies
3.1k
views
7 follow
Venter Genome Vcf
vcf
updated 2 days ago by ▴ 20 • written 10.1 years ago by ▴ 980
0
votes
0
replies
116
views
16S analysis for specie of bacteria identification
Species-identification 16S Kraken2
updated 2 days ago by 44k • written 2 days ago by ▴ 10
4
votes
1
reply
184
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq padj p-value
updated 2 days ago by 14k • written 2 days ago by • 0
0
votes
0
replies
99
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 2 days ago by 142k • written 2 days ago by • 0
0
votes
3
replies
312
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell RNA-Seq single
updated 2 days ago by 82k • written 2 days ago by • 0
0
votes
1
reply
159
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2 ATACseq DiffBind
updated 2 days ago by ★ 17k • written 2 days ago by • 0
0
votes
2
replies
208
views
What do the transcript variant # mean in RefSeq?
refseq
updated 2 days ago by 44k • written 2 days ago by ▴ 750
4
votes
6
replies
385
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body expression atlas
2 days ago by Shicheng Guo ★ 9.4k
1
vote
3
replies
281
views
Error when looping over multiple columns in a data frame in R
Statistics R
updated 2 days ago by ▴ 910 • written 3 days ago by ▴ 30
2
votes
0
replies
171
views
Job: Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics Sequencing Sweden Stockholm SciLifeLab
2 days ago by Matthias Zepper 4.6k
0
votes
1
reply
133
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5 Fossil
updated 2 days ago by 44k • written 2 days ago by ▴ 10
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS Bismark DNA-methylation
updated 2 days ago by ★ 2.9k • written 3.9 years ago by ▴ 40
0
votes
0
replies
162
views
Job: 2 PhD Students in single-cell bioinformatics
PhD Genomics single-cell NGS
1 day ago by mtabaka • 0
0
votes
1
reply
139
views
minfi::getQC - badsamplecutoff 10.5
getqc minfi methylation EPICv2
updated 2 days ago by ★ 2.9k • written 2 days ago by • 0
0
votes
2
replies
658
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc ewas minfi
updated 2 days ago by • 0 • written 10 months ago by • 0
2
votes
5
replies
285
views
Z score
Z-score
updated 2 days ago by 44k • written 2 days ago by ▴ 60
2
votes
6
replies
306
views
Error with BiocParallel. No barcodes files found
Barcodes scRNA-seq SingleCellExperiment
1 day ago by bio_info ▴ 10
3
votes
3
replies
222
views
Unexpected read length from NGS
NGS Illumina
1 day ago by QX • 0
679 results • Page 1 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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