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45 results • Page
1 of 1
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Votes
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0
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0
replies
11
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
30 minutes ago by
hashim.rana11
▴ 20
0
votes
0
replies
20
views
Forum:
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
2 hours ago by
F110152169
• 0
8
votes
9
replies
3.0k
views
7 follow
Venter Genome Vcf
vcf
updated 2 hours ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
0
votes
9
replies
497
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
updated 5 hours ago by
ATpoint
82k • written 6 days ago by
hannes.bongartz
• 0
0
votes
0
replies
45
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 6 hours ago by
Ram
44k • written 7 hours ago by
Christopher
▴ 10
4
votes
1
reply
113
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 7 hours ago by
swbarnes2
14k • written 12 hours ago by
May Ling
• 0
0
votes
0
replies
40
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 7 hours ago by
GenoMax
142k • written 7 hours ago by
jway
• 0
0
votes
3
replies
155
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 5 hours ago by
ATpoint
82k • written 7 hours ago by
shahzaibali
• 0
0
votes
1
reply
99
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 8 hours ago by
jared.andrews07
★ 17k • written 12 hours ago by
atan
• 0
0
votes
2
replies
137
views
What do the transcript variant # mean in RefSeq?
refseq
updated 8 hours ago by
Ram
44k • written 11 hours ago by
curious
▴ 750
4
votes
6
replies
306
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
8 hours ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
209
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 6 hours ago by
Jeremy
▴ 910 • written 1 day ago by
Mohamed Samir
▴ 30
2
votes
0
replies
95
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
12 hours ago by
Matthias Zepper
4.6k
0
votes
1
reply
79
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 12 hours ago by
Ram
44k • written 12 hours ago by
a.bibek52
▴ 10
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 12 hours ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
85
views
Job:
2 PhD Students in single-cell bioinformatics
NGS
11 hours ago by
mtabaka
• 0
0
votes
1
reply
87
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 12 hours ago by
Papyrus
★ 2.9k • written 12 hours ago by
June
• 0
0
votes
2
replies
609
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 12 hours ago by
June
• 0 • written 10 months ago by
rkb965
• 0
2
votes
5
replies
227
views
Z score
Z-score
updated 12 hours ago by
Ram
44k • written 19 hours ago by
Akash D
▴ 60
1
vote
5
replies
203
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
updated 12 hours ago by
Pierre Lindenbaum
162k • written 16 hours ago by
NTerway
• 0
1
vote
2
replies
134
views
Unexpected read length from NGS
NGS
Illumina
updated 15 hours ago by
ATpoint
82k • written 17 hours ago by
QX
• 0
0
votes
0
replies
58
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
15 hours ago by
adarsh_pp
▴ 40
1
vote
6
replies
277
views
samtools write-index
samtools
updated 16 hours ago by
aw7
▴ 310 • written 2 days ago by
LucisTheFather
• 0
0
votes
2
replies
196
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 17 hours ago by
i.sudbery
19k • written 1 day ago by
Varsha
• 0
1
vote
2
replies
130
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 15 hours ago by
ATpoint
82k • written 18 hours ago by
egascon
• 0
0
votes
0
replies
59
views
GWAS or QTL mapping in RIL population
GWAS
RIL
17 hours ago by
韩雨
• 0
0
votes
0
replies
66
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 12 hours ago by
Ram
44k • written 17 hours ago by
emmanouil.a
▴ 120
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 12 hours ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
241
views
GWAS Phenotypes
GWAS
updated 18 hours ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.1k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 18 hours ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
0
votes
1
reply
98
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 15 hours ago by
GenoMax
142k • written 18 hours ago by
azeu
• 0
0
votes
0
replies
49
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
19 hours ago by
Linus
• 0
7
votes
3
replies
13k
views
Z score in RNAseq
RNA-Seq
Zscore
updated 19 hours ago by
Akash D
▴ 60 • written 6.5 years ago by
rob.costa1234
▴ 310
0
votes
1
reply
118
views
Free AI for R programming
R
updated 12 hours ago by
Ram
44k • written 19 hours ago by
mohamadzare6022
▴ 10
7
votes
13
replies
795
views
7 follow
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 13 hours ago by
i.sudbery
19k • written 4 weeks ago by
Estevão
▴ 10
0
votes
0
replies
83
views
Extracting haplotype-specific annotations from splicing graph
vg
23 hours ago by
Juhyun
• 0
0
votes
1
reply
111
views
Flag multiple filtering steps on VCF files using VEP
VEP
VCF
updated 12 hours ago by
Ram
44k • written 1 day ago by
avelarbio46
▴ 30
0
votes
0
replies
99
views
Subset of ATAC-seq peaks has high variance
atac-seq
edgeR
R
normalization
21 hours ago by
Tim
• 0
2
votes
6
replies
279
views
How to get the ratio of allele counts from GATK derived VCF file?
Freebayes
GATK
SNP
VCF
20 hours ago by
anikcropscience
▴ 230
2
votes
4
replies
1.2k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
16 hours ago by
Aspire
▴ 330
0
votes
2
replies
129
views
CreateSeuratObject taking very long
seurat
just now by
eae6d2e7
• 0
0
votes
4
replies
366
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
7 hours ago by
mavy
▴ 10
1
vote
4
replies
388
views
some error in building kraken2 database
metagenome
kraken2
updated 15 hours ago by
GenoMax
142k • written 4 weeks ago by
Art1ess
• 0
22
votes
15
replies
10k
views
12 follow
Alternatives To Liftover
liftover
genome
mapping
updated 22 hours ago by
Thanujay S
• 0 • written 12.5 years ago by
woemler
▴ 170
45 results • Page
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Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
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Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
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Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
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Comment: CreateSeuratObject taking very long
by
eae6d2e7
• 0
Thank you for your reply! I followed your advice to convert to sparse matrix first but I got this error Error in Matrix::sparseMatrix(raw_…
Answer: Venter Genome Vcf
by
ericrkofman
▴ 20
I can't find an hg38 version, and the old VCF seems to be of a different header format so I am having difficulty converting it to hg38 from…
Comment: What is a good way to do gene differentials in single cell data where one group
by
ATpoint
82k
Preferred if you have true biological replicates. Can still be combined with my subsetting strategy, like use 100x different cells for the …
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
by
ATpoint
82k
```r set.seed(1) m = matrix(rnorm(100), nrow = 10) rownames(m) = 1:10 # normal ha = rowAnnotation(foo = anno_mark(at=1:nrow(m), labels=row…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
44k
Please do not add answers unless you're actually answering the question. I've moved your post to a comment.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
I still cannot find a way. It seems to be an easy to solve issue and I was trying any possible combination with the aforementioned gp=gpar(…
Comment: What is a good way to do gene differentials in single cell data where one group
by
fracarb8
★ 1.6k
I would probably use a pseudobulk approach.
Comment: Error when looping over multiple columns in a data frame in R
by
Jeremy
▴ 910
`cutpoint_results[[col_name]]` adds each new cut point to the list entitled "cutpoint_results", while keeping the original column names fr…
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
by
swbarnes2
14k
Never use uncorrected p-values with RNASeq. Your PCA is suggesting that your sample groups are not very different, and the DEG tests con…
Comment: What is a good way to do gene differentials in single cell data where one group
by
ATpoint
82k
I would keep it transparent. Do DE by subsetting large to small group. Do that randomly many times, then either average stats or use some s…
Answer: Trying to understand warning from MACS2 about too few paired peaks and differing
by
jared.andrews07
★ 17k
Without looking at the actual sequence for each genome, my guess is that the Echinobase reference just matches much more closely to the org…
Comment: What do the transcript variant # mean in RefSeq?
by
Ram
44k
> It does not seem to be the longest transcript. Is it the canonical transcript? Longest == canonical. If you're looking for the transcrip…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
Shicheng Guo
★ 9.4k
Hi ATpoint, Thank you for your responses. My apologies if my inquiries have seemed one-sided. I greatly value the collaborative spirit of t…
Comment: Mouse or Rat Gene Expression Data Similar to GTEx
by
ATpoint
82k
Team? A team helps each other out. You only take help by posting your regular lazy do-my-work questions and never give anything back. Save …
Comment: What do the transcript variant # mean in RefSeq?
by
GenoMax
142k
> What do these correspond to? It does not seem to be the longest transcript. Is it the canonical transcript? Those are just different tra…
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