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699 results • Page
3 of 14
Sort: Rank
Rank
Views
Votes
Replies
0
votes
2
replies
183
views
vcf phasing
beagle
WhatsHap
phasing
1 day ago by
safeassli
▴ 10
0
votes
2
replies
209
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
3 days ago by
sainavyav22
• 0
0
votes
1
reply
610
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 3 days ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
194
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 3 days ago by
Ram
44k • written 3 days ago by
Sony
▴ 10
0
votes
3
replies
208
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 3 days ago by
Ram
44k • written 3 days ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
100
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 3 days ago by
Ram
44k • written 3 days ago by
ev97
▴ 20
0
votes
1
reply
144
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 3 days ago by
marco.barr
▴ 130 • written 3 days ago by
sooni
▴ 20
0
votes
1
reply
106
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 3 days ago by
GenoMax
142k • written 3 days ago by
jinyi
• 0
0
votes
0
replies
83
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
3 days ago by
V_Vibes
• 0
0
votes
0
replies
178
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 3 days ago by
Ram
44k • written 3 days ago by
JorgeVallejo
▴ 20
0
votes
0
replies
105
views
transcriptome annotation
annotation
trinity
transcriptome
updated 3 days ago by
Ram
44k • written 3 days ago by
Asim Bin Arshad
• 0
0
votes
5
replies
234
views
Why most genes have high padj values
RNA-seq
DEG
updated 3 days ago by
Ram
44k • written 3 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 3 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
150
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 3 days ago by
zx8754
11k • written 3 days ago by
Ali
• 0
0
votes
4
replies
257
views
GO analysis: p-value range
GO
R
updated 3 days ago by
Matthias Zepper
4.6k • written 4 days ago by
sooni
▴ 20
1
vote
2
replies
236
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 2 days ago by
colindaven
6.4k • written 4 days ago by
Dr.
• 0
0
votes
3
replies
243
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 3 days ago by
GenoMax
142k • written 4 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
103
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
4 days ago by
Maryam
• 0
0
votes
4
replies
346
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
4 days ago by
Bibi
• 0
1
vote
2
replies
358
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 4 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
115
views
handling bio replicates for chromHMM
replicates
chromHMM
4 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
105
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
4 days ago by
DGTool
▴ 20
1
vote
1
reply
183
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 4 days ago by
ATpoint
82k • written 4 days ago by
rj.rezwan
• 0
0
votes
2
replies
329
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
4 days ago by
Ezequiel
• 0
2
votes
0
replies
192
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
4 days ago by
micah
▴ 30
0
votes
0
replies
121
views
problems in installing rDock
rDock
updated 3 days ago by
Ram
44k • written 4 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 4 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
731
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 4 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
385
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 days ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
142
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 5 days ago by
Pierre Lindenbaum
162k • written 5 days ago by
Mohamed Samir
▴ 30
0
votes
0
replies
152
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
5 days ago by
Moinuddin
• 0
0
votes
1
reply
193
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Jacek
▴ 20
2
votes
1
reply
265
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 5 days ago by
Gordon Smyth
★ 7.2k • written 6 days ago by
marineandriot
• 0
0
votes
0
replies
154
views
How can i use ESM-1v ?
VEP
ESM-1v
5 days ago by
Meto
• 0
0
votes
0
replies
162
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Long
• 0
2
votes
3
replies
350
views
Trimming tool
Trimming
updated 3 days ago by
Ram
44k • written 6 days ago by
GeneC
• 0
0
votes
0
replies
153
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
6 days ago by
kilcdincer
▴ 10
0
votes
2
replies
280
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 6 days ago by
LauferVA
4.2k • written 6 days ago by
ijarne
• 0
0
votes
0
replies
172
views
genomic region of transcription factor
search
HOMER
motif
6 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
398
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 6 days ago by
dthorbur
★ 2.0k • written 7 days ago by
BATMAN
• 0
0
votes
0
replies
159
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 6 days ago by
GenoMax
142k • written 6 days ago by
yura.grabovska
▴ 90
4
votes
9
replies
653
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 2 days ago by
marco.barr
▴ 130 • written 8 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
215
views
constructing pangenome through psvcp
psvcp
pangenome
5 days ago by
analyst
▴ 50
1
vote
6
replies
366
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
2 days ago by
Umer
▴ 50
0
votes
4
replies
378
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 5 days ago by
txema.heredia
▴ 130 • written 7 days ago by
Ngrin
• 0
4
votes
9
replies
527
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
6 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
271
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 6 days ago by
Pierre Lindenbaum
162k • written 6 days ago by
melissachua90
▴ 70
0
votes
0
replies
140
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
6 days ago by
Varsha
• 0
0
votes
1
reply
466
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 6 days ago by
GenoMax
142k • written 6 days ago by
huxiangyulove
• 0
0
votes
0
replies
156
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
7 days ago by
O.rka
▴ 720
699 results • Page
3 of 14
Recent Votes
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
Random Access remote BAM files
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
C: Converting narrowPeak to bed
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
Answer: PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while ad
A: VCF files: Change Chromosome Notation
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Recent Awards •
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Teacher
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• 0
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142k
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Recent Replies
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…
Answer: Mouse or Rat Gene Expression Data Similar to GTEx
by
jared.andrews07
★ 17k
MGI has a [Gene Expression Database](https://www.informatics.jax.org/expression.shtml) that'll largely get you what you want.
Comment: Difference in Bismark output methylation call files and coverage files
by
Papyrus
★ 2.9k
Your files end in `CpG_report` so they are the "genome-wide cytosine report output". If you look at the [Bismark documentation][1] you will…
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