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672 results • Page
1 of 14
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Views
Votes
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0
votes
0
replies
23
views
Tubemap multiseq
vg
2 hours ago by
karciharun42
• 0
0
votes
0
replies
45
views
Facing problem with single cell rna seq annotation using singleR
annotation
singleR
scRNAseq
5 hours ago by
sc_analysis
• 0
5
votes
4
replies
5.8k
views
Attempt to set 'rownames' on an object with no dimensions
R
microbiome
spieceasi
updated 1 hour ago by
GenoMax
142k • written 3.6 years ago by
ks.sholohova
▴ 30
0
votes
0
replies
52
views
News:
Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
PopulationGenomics
GenotypeLikelihoods
Low-Coverage
ANGSD
10 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
87
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
10 hours ago by
Sara
▴ 30
0
votes
0
replies
84
views
How to decrease the motif score?
scores
Motif
1 day ago by
Hadia
• 0
0
votes
0
replies
83
views
immuCell Abundance infiltrate
ImmuCell
Abundance
infiltrate
updated 1 day ago by
Pierre Lindenbaum
162k • written 1 day ago by
elbakri.fatimazahrae
• 0
0
votes
2
replies
149
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 2 hours ago by
LauferVA
4.2k • written 1 day ago by
carolofharvest
▴ 40
0
votes
0
replies
81
views
MaxEntScan for rMATS results
MaxEntScan
rMATS
1 day ago by
adi.gershon1
• 0
0
votes
0
replies
227
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
93
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
179
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
indexing
salmon
updated 1 day ago by
Rob
6.6k • written 1 day ago by
Tonya S.
▴ 10
0
votes
3
replies
311
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
11
replies
702
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 3 hours ago by
Ram
44k • written 9 days ago by
hannes.bongartz
• 0
0
votes
0
replies
111
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
2 days ago by
marco.barr
▴ 130
0
votes
0
replies
105
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
2 days ago by
niconps14
• 0
1
vote
5
replies
299
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 6 hours ago by
Pierre Lindenbaum
162k • written 2 days ago by
QX
• 0
2
votes
5
replies
311
views
Harmony integration group.by.var parameter
single-cell
harmony
6 hours ago by
Picasa
▴ 640
2
votes
1
reply
158
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 2 days ago by
Jeremy Leipzig
22k • written 2 days ago by
liaotsungjen
▴ 10
0
votes
0
replies
97
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 2 days ago by
Ram
44k • written 2 days ago by
Alessia
• 0
1
vote
3
replies
244
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 1 day ago by
Bastien Hervé
5.3k • written 2 days ago by
Sara
▴ 30
0
votes
1
reply
142
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 2 days ago by
Ram
44k • written 2 days ago by
garcesj
▴ 50
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 2 days ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
1
reply
361
views
LDhat lookup table
LDhat
updated 2 days ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
0
replies
115
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
2 days ago by
irebekah.c
• 0
0
votes
0
replies
107
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 2 days ago by
Ram
44k • written 2 days ago by
kl
▴ 10
0
votes
5
replies
222
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
2 days ago by
Deepthi
• 0
0
votes
1
reply
223
views
Annotating single cell data automatically
single-cell
updated 2 days ago by
Ram
44k • written 4 weeks ago by
Gerard
• 0
1
vote
4
replies
285
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
2 days ago by
sc_analysis
• 0
0
votes
1
reply
171
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 2 days ago by
Bastien Hervé
5.3k • written 2 days ago by
bio_info
▴ 10
3
votes
4
replies
453
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 2 days ago by
fracarb8
★ 1.7k • written 10 days ago by
txema.heredia
▴ 130
0
votes
0
replies
131
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
2 days ago by
doramora
▴ 10
0
votes
0
replies
106
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
2 days ago by
Emily
▴ 20
2
votes
3
replies
233
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
161
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 2 days ago by
Pierre Lindenbaum
162k • written 2 days ago by
Maksim
• 0
1
vote
2
replies
252
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
2 days ago by
F110152169
• 0
8
votes
9
replies
3.1k
views
7 follow
Venter Genome Vcf
vcf
updated 2 days ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
0
votes
0
replies
137
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 2 days ago by
Ram
44k • written 2 days ago by
Christopher
▴ 10
4
votes
1
reply
205
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
swbarnes2
14k • written 3 days ago by
May Ling
• 0
0
votes
0
replies
117
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jway
• 0
0
votes
3
replies
330
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
ATpoint
82k • written 2 days ago by
shahzaibali
• 0
0
votes
1
reply
179
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
jared.andrews07
★ 17k • written 3 days ago by
atan
• 0
0
votes
2
replies
230
views
What do the transcript variant # mean in RefSeq?
refseq
updated 2 days ago by
Ram
44k • written 3 days ago by
curious
▴ 750
4
votes
6
replies
407
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
300
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 2 days ago by
Jeremy
▴ 910 • written 3 days ago by
Mohamed Samir
▴ 30
2
votes
0
replies
194
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
3 days ago by
Matthias Zepper
4.6k
0
votes
1
reply
155
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 3 days ago by
Ram
44k • written 3 days ago by
a.bibek52
▴ 10
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 3 days ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
186
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
2 days ago by
mtabaka
• 0
0
votes
1
reply
156
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 3 days ago by
Papyrus
★ 2.9k • written 3 days ago by
June
• 0
672 results • Page
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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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Comment: Setting a threshold on gene expression for subsetting (scRNA-seq)
by
LauferVA
4.2k
Generally, I cannot advise this in the abstract. The thing is, depending on the treatment group and so forth, there are some transcripts th…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: Getting differential ChIP-seq peaks between conditions after calling consensus p
by
Alexandra
• 0
Thank you for your response! Interesting paper.
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!
Comment: 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 =…
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
Comment: 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 …
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