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Illumina methylation EPIC V2 array
ewas methylation enrichment missMethyl EPIC
updated 9 minutes ago by ▴ 40 • written 8 months ago by • 0
0
votes
0
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23
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How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
SharedVariants Upset
updated 1 hour ago by 142k • written 1 hour ago by • 0
0
votes
2
replies
87
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta identical sequences.
updated 1 hour ago by 142k • written 7 hours ago by ▴ 10
0
votes
3
replies
85
views
GATK Structural Variants Pipeline - Steps
SV VariantCalling GATK
1 hour ago by Bioinformatics_begginner ▴ 20
0
votes
0
replies
34
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat 10X scRNAseq read10x singlecell
3 hours ago by ev97 ▴ 20
0
votes
1
reply
58
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy GO R
updated 1 hour ago by ▴ 130 • written 4 hours ago by ▴ 20
0
votes
1
reply
51
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 34 minutes ago by 142k • written 4 hours ago by • 0
799
votes
167
replies
144k
views
109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.8k • written 7.5 years ago by 100k
0
votes
0
replies
38
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA ENCORI curl microRNA starBase
5 hours ago by V_Vibes • 0
0
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0
replies
52
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How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression confounding
5 hours ago by JorgeVallejo ▴ 20
0
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0
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53
views
transcriptome annotation
annotation transcriptome cone trinity snails conus genome
6 hours ago by Asim Bin Arshad • 0
0
votes
4
replies
133
views
Why most genes have high padj values
deg padj bulkRNA
4 hours ago by mnx0723 • 0
7
votes
14
replies
2.8k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 7 hours ago by ▴ 30 • written 3.1 years ago by • 0
0
votes
1
reply
82
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 7 hours ago by 82k • written 9 hours ago by ▴ 100
0
votes
1
reply
94
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs PCA GBS LINUX r
updated 5 hours ago by 11k • written 10 hours ago by • 0
0
votes
1
reply
82
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 5 hours ago by ▴ 130 • written 12 hours ago by ▴ 20
0
votes
4
replies
180
views
GO analysis: p-value range
GO R
updated 3 hours ago by 4.6k • written 14 hours ago by ▴ 20
1
vote
0
replies
71
views
News: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk PlatformPresentation
14 hours ago by Dr. • 0
0
votes
3
replies
185
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq seqtk extractionproblem
updated 2 hours ago by 142k • written 1 day ago by • 0
0
votes
0
replies
70
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R Mean Affymetrix Probes Grouping
15 hours ago by Maryam • 0
1
vote
7
replies
341
views
Add stats to the plot
R stats plotting
updated 4 hours ago by ▴ 130 • written 1 day ago by • 0
0
votes
4
replies
287
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
16 hours ago by Bibi • 0
1
vote
2
replies
317
views
is there a tool to recover corrupted fastq files
fastq short-read
updated 17 hours ago by • 0 • written 3 months ago by ▴ 60
0
votes
0
replies
81
views
handling bio replicates for chromHMM
replicates chromHMM
20 hours ago by Hasan_Daaboul • 0
0
votes
0
replies
72
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell communication ligand-receptor self-regulation
20 hours ago by DGTool ▴ 20
0
votes
1
reply
133
views
geom_bar issue in ggplot2 with xlim()
geom_bar ggplot2 statistics R
updated 21 hours ago by 82k • written 23 hours ago by • 0
0
votes
2
replies
282
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix RNA-Seq Limma DESeq2 edgeR
23 hours ago by Ezequiel • 0
2
votes
0
replies
157
views
Tool: Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap alignment NGMLR
1 day ago by micah ▴ 30
0
votes
0
replies
93
views
problems in installing rDock
rDock make Installation Error
1 day 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 1 day ago by ▴ 30 • written 8 months ago by ▴ 870
1
vote
2
replies
698
views
Checking chromosome builds for genotyping data
GWAS Liftover PLINK
updated 1 day ago by • 0 • written 2.6 years ago by • 0
1
vote
1
reply
312
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx cibersort error RNA-Seq deconvolution
updated 1 day ago by • 0 • written 3 months ago by ▴ 10
0
votes
0
replies
115
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 1 day ago by 161k • written 1 day ago by ▴ 20
0
votes
0
replies
119
views
Tera-scale metagenomic coassembly tool
co-assembly Metagenomics
2 days ago by Moinuddin • 0
0
votes
1
reply
162
views
Broad and Narrow peaks
ATAC ChIP seq
updated 2 days ago by 82k • written 2 days ago by ▴ 20
2
votes
1
reply
227
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 1 day ago by ★ 7.2k • written 2 days ago by • 0
0
votes
0
replies
124
views
How can i use ESM-1v ?
VEP ESM-1v
2 days ago by Meto • 0
0
votes
0
replies
134
views
Cell type annotation mixed with other type cells
cell annotation.
updated 2 days ago by 142k • written 2 days ago by • 0
0
votes
2
replies
238
views
Trimming tool
Trimmer tool
updated 2 days ago by ▴ 60 • written 2 days ago by • 0
0
votes
0
replies
132
views
sci-RNA-seq
cell single seurat sci-rna-seq counts
2 days ago by kilcdincer ▴ 10
0
votes
2
replies
242
views
GG Sankey plot
GO sankey_plot gglpot
updated 2 days ago by 4.2k • written 2 days ago by • 0
0
votes
0
replies
154
views
genomic region of transcription factor
search HOMER motif
2 days ago by qudrat.nii ▴ 10
1
vote
5
replies
364
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 2 days ago by ★ 2.0k • written 3 days ago by • 0
0
votes
6
replies
353
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
2 days ago by hannes.bongartz • 0
0
votes
0
replies
139
views
Understanding behaviour of SCTransform in Seurat
Seurat scRNASeq normalization
updated 3 days ago by 142k • written 3 days ago by ▴ 90
4
votes
7
replies
533
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 3 days ago by ▴ 130 • written 4 days ago by ▴ 20
1
vote
1
reply
196
views
constructing pangenome through psvcp
psvcp pangenome
1 day ago by analyst ▴ 50
0
votes
3
replies
264
views
What marks a De-Novo Genome assembly as FAILED?
nanopore denovo illumina assembly genome
updated 8 hours ago by ▴ 20 • written 3 days ago by ▴ 50
0
votes
4
replies
345
views
How to handle duplicated genes in TCGA data?
TCGA GDC mRNA
updated 2 days ago by ▴ 130 • written 3 days ago by • 0
4
votes
9
replies
490
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
3 days ago by Gabriel R. ★ 2.9k
117,028 results • Page 1 of 2341
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Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: How do you generate TMM normalized counts using EdgeR?
Answer: How do you generate TMM normalized counts using EdgeR?
Analysing Microarray Data In Bioconductor
Answer: Q: GenomeScope input and how to interpret the results
Answer: How to find tandem duplications pattern in a DNA sequence
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Answer: Illumina methylation EPIC V2 array by fu_entomology ▴ 40
We have been using SeSAMe, it works well for the most part. They have an enrichment tool called KnowYourCG. You can check it out their vign…
Answer: How to find identical sequences in genome fasta file (by Python or any possible by GenoMax 142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway by marco.barr ▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps by Bioinformatics_begginner ▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by GenoMax 142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps by Pierre Lindenbaum 161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps by DGTool ▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range by Matthias Zepper 4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range by marco.barr ▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range by sooni ▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values by mnx0723 • 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version) by jinyi • 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot by marco.barr ▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds by marco.barr ▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot by Ghada • 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
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