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5
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4
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5.7k
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Attempt to set 'rownames' on an object with no dimensions
R microbiome spieceasi
updated 2 hours ago by • 0 • written 3.6 years ago by ▴ 30
0
votes
0
replies
33
views
News: Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
PopulationGenomics GenotypeLikelihoods Low-Coverage ANGSD
4 hours ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
75
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat Pseudobulk single-cell DESeq2 scRNA
3 hours ago by Sara ▴ 30
0
votes
0
replies
76
views
How to decrease the motif score?
scores Motif
21 hours ago by Hadia • 0
0
votes
0
replies
76
views
immuCell Abundance infiltrate
ImmuCell Abundance infiltrate
updated 21 hours ago by 162k • written 22 hours ago by • 0
0
votes
1
reply
121
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 1 day ago by 82k • written 1 day ago by ▴ 40
0
votes
0
replies
71
views
MaxEntScan for rMATS results
MaxEntScan rMATS
1 day ago by adi.gershon1 • 0
0
votes
0
replies
174
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker. MAKER. annotation.
1 day ago by Sony ▴ 10
0
votes
0
replies
85
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
4
votes
2
replies
168
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq stringtie indexing salmon
updated 1 day ago by 6.6k • written 1 day ago by ▴ 10
0
votes
3
replies
291
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
666
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r ComplexHeatmap
1 day ago by hannes.bongartz • 0
0
votes
0
replies
99
views
perl Error - needLargeMem Bigwig
Bigwig perl mitosalt
1 day ago by marco.barr ▴ 130
0
votes
0
replies
94
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
1 day ago by niconps14 • 0
1
vote
5
replies
240
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated just now by 162k • written 2 days ago by • 0
2
votes
5
replies
274
views
Harmony integration group.by.var parameter
single-cell harmony
just now by Picasa ▴ 640
2
votes
1
reply
148
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
votes
0
replies
90
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
235
views
How to calculate cell type frequency between two groups in single cell data
Seurat single-cell sc-RNA cell-type
updated 23 hours ago by 5.3k • written 2 days ago by ▴ 30
0
votes
1
reply
133
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
354
views
LDhat lookup table
LDhat
updated 1 day ago by 44k • written 11 months ago by ▴ 10
0
votes
0
replies
107
views
BAM to Bedgraph creating an empty file
Bisulfite-seq bismark
1 day ago by irebekah.c • 0
0
votes
0
replies
99
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 2 days ago by ▴ 10
0
votes
5
replies
214
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
214
views
Annotating single cell data automatically
single-cell
updated 1 day ago by 44k • written 4 weeks ago by • 0
1
vote
4
replies
275
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
164
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat scRNA-seq UMAP
updated 1 day ago by 5.3k • written 2 days ago by ▴ 10
3
votes
4
replies
444
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 2 days ago by ★ 1.7k • written 9 days ago by ▴ 130
0
votes
0
replies
123
views
R code for KEGG pathways output
KEGGREST dplyr KEGG R
2 days ago by doramora ▴ 10
0
votes
0
replies
98
views
finding highly divergent orthologs using exonerate
ortholog Exonerate evolution
2 days ago by Emily ▴ 20
2
votes
3
replies
224
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity mtDNA PacBio
2 days ago by hashim.rana11 ▴ 20
0
votes
1
reply
153
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 2 days ago by 162k • written 2 days ago by • 0
1
vote
2
replies
243
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
129
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
197
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
109
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
323
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
172
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
221
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
398
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
292
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
184
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
145
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
175
views
Job: 2 PhD Students in single-cell bioinformatics
PhD Genomics single-cell NGS
2 days ago by mtabaka • 0
0
votes
1
reply
149
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
669
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
296
views
Z score
Z-score
updated 2 days ago by 44k • written 3 days ago by ▴ 60
180 results • Page 1 of 4
Recent Votes
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
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?
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Recent Replies
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website by Pierre Lindenbaum 162k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
@jaredandrews07 If I integrate using Donor: ```R RunHarmony(seu_obj, group.by.vars = c("Donor_ID")) ``` Should I also normalize my data…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website by QX • 0
thank you so much!
Answer: Attempt to set 'rownames' on an object with no dimensions by elbakri.fatimazahrae • 0
hello everyone, I got the same error for a function immuCellAI_new; result <- ImmuCellAI_new(countData = expr_data_log22, data_type = "rnas…
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!
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