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714 results • Page
2 of 15
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Votes
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0
votes
2
replies
199
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
1 day ago by
sainavyav22
• 0
0
votes
1
reply
606
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 1 day ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
185
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 1 day ago by
Ram
44k • written 2 days ago by
Sony
▴ 10
0
votes
3
replies
198
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 1 day ago by
Ram
44k • written 1 day ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
91
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
ev97
▴ 20
0
votes
1
reply
137
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 1 day ago by
marco.barr
▴ 130 • written 1 day ago by
sooni
▴ 20
0
votes
1
reply
104
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jinyi
• 0
0
votes
0
replies
81
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
1 day ago by
V_Vibes
• 0
0
votes
0
replies
149
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 1 day ago by
Ram
44k • written 1 day ago by
JorgeVallejo
▴ 20
0
votes
0
replies
100
views
transcriptome annotation
annotation
trinity
transcriptome
updated 1 day ago by
Ram
44k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
225
views
Why most genes have high padj values
RNA-seq
DEG
updated 1 day ago by
Ram
44k • written 1 day 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 2 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
146
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 1 day ago by
zx8754
11k • written 2 days ago by
Ali
• 0
0
votes
4
replies
246
views
GO analysis: p-value range
GO
R
updated 1 day ago by
Matthias Zepper
4.6k • written 2 days ago by
sooni
▴ 20
1
vote
2
replies
230
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 22 hours ago by
colindaven
6.4k • written 2 days ago by
Dr.
• 0
0
votes
3
replies
238
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 1 day ago by
GenoMax
142k • written 3 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
100
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
2 days ago by
Maryam
• 0
0
votes
4
replies
332
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
2 days ago by
Bibi
• 0
1
vote
2
replies
353
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 2 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
112
views
handling bio replicates for chromHMM
replicates
chromHMM
2 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
104
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
2 days ago by
DGTool
▴ 20
1
vote
1
reply
173
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 2 days ago by
ATpoint
82k • written 2 days ago by
rj.rezwan
• 0
0
votes
2
replies
319
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
2 days ago by
Ezequiel
• 0
2
votes
0
replies
188
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
2 days ago by
micah
▴ 30
0
votes
0
replies
120
views
problems in installing rDock
rDock
updated 1 day ago by
Ram
44k • written 3 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 3 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
726
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 3 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
381
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 12 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
139
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
145
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
3 days ago by
Moinuddin
• 0
0
votes
1
reply
187
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Jacek
▴ 20
2
votes
1
reply
260
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 3 days ago by
Gordon Smyth
★ 7.2k • written 4 days ago by
marineandriot
• 0
0
votes
0
replies
149
views
How can i use ESM-1v ?
VEP
ESM-1v
4 days ago by
Meto
• 0
0
votes
0
replies
158
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Long
• 0
2
votes
3
replies
336
views
Trimming tool
Trimming
updated 1 day ago by
Ram
44k • written 4 days ago by
GeneC
• 0
0
votes
0
replies
151
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
4 days ago by
kilcdincer
▴ 10
0
votes
2
replies
270
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 4 days ago by
LauferVA
4.2k • written 4 days ago by
ijarne
• 0
0
votes
0
replies
166
views
genomic region of transcription factor
search
HOMER
motif
4 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
390
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 4 days ago by
dthorbur
★ 2.0k • written 5 days ago by
BATMAN
• 0
0
votes
6
replies
381
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
4 days ago by
hannes.bongartz
• 0
0
votes
0
replies
155
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 4 days ago by
GenoMax
142k • written 4 days ago by
yura.grabovska
▴ 90
4
votes
9
replies
642
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 21 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
209
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
1
vote
6
replies
358
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
19 hours ago by
Umer
▴ 50
0
votes
4
replies
367
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 3 days ago by
txema.heredia
▴ 130 • written 5 days ago by
Ngrin
• 0
4
votes
9
replies
514
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
4 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
265
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
melissachua90
▴ 70
0
votes
0
replies
138
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
5 days ago by
Varsha
• 0
0
votes
1
reply
461
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 4 days ago by
GenoMax
142k • written 5 days ago by
huxiangyulove
• 0
0
votes
0
replies
153
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
5 days ago by
O.rka
▴ 720
714 results • Page
2 of 15
Recent Votes
Answer: geom_bar issue in ggplot2 with xlim()
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GO analysis: Different results EnrichGO vs ShinyGO
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
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Recent Replies
Comment: Splitting query fasta file for Diamond Blastp make the process faster?
by
kmat
• 0
Thank you for your quick responce. Sorry for the lack of explanation. Here are some supplementary details regarding the parameters of Diam…
Answer: Splitting query fasta file for Diamond Blastp make the process faster?
by
Mensur Dlakic
★ 27k
There are several pieces of information we are missing here. Did you specify that all 96 threads be used? If so, are all of them being used…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",…
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