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319 results • Page
1 of 7
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Votes
Replies
0
votes
1
reply
72
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
Bjorn
• 0
0
votes
3
replies
177
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 3 hours ago by
marco.barr
▴ 130 • written 23 hours ago by
Mohamed Samir
▴ 20
0
votes
0
replies
51
views
vcf phasing
beagle
WhatsHap
phasing
10 hours ago by
safeassli
▴ 10
0
votes
0
replies
56
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 7 hours ago by
Ram
43k • written 13 hours ago by
ev97
▴ 20
0
votes
1
reply
103
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 11 hours ago by
marco.barr
▴ 130 • written 14 hours ago by
sooni
▴ 20
0
votes
1
reply
75
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 11 hours ago by
GenoMax
142k • written 15 hours ago by
jinyi
• 0
0
votes
0
replies
56
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
16 hours ago by
V_Vibes
• 0
0
votes
0
replies
86
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 4 hours ago by
Ram
43k • written 16 hours ago by
JorgeVallejo
▴ 20
0
votes
0
replies
71
views
transcriptome annotation
annotation
trinity
transcriptome
updated 9 hours ago by
Ram
43k • written 16 hours ago by
Asim Bin Arshad
• 0
0
votes
5
replies
197
views
Why most genes have high padj values
RNA-seq
DEG
updated 7 hours ago by
Ram
43k • written 17 hours ago by
mnx0723
• 0
0
votes
1
reply
101
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 18 hours ago by
ATpoint
82k • written 20 hours ago by
Pegasus
▴ 100
0
votes
1
reply
116
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 16 hours ago by
zx8754
11k • written 21 hours ago by
Ali
• 0
0
votes
4
replies
217
views
GO analysis: p-value range
GO
R
updated 14 hours ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
83
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
1 day ago by
Maryam
• 0
1
vote
7
replies
385
views
Add stats to the plot
R
1 day ago by
Ghada
• 0
0
votes
4
replies
304
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
0
votes
0
replies
97
views
handling bio replicates for chromHMM
replicates
chromHMM
1 day ago by
Hasan_Daaboul
• 0
0
votes
0
replies
88
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
1 day ago by
DGTool
▴ 20
0
votes
0
replies
105
views
problems in installing rDock
rDock
updated 4 hours ago by
Ram
43k • written 1 day ago by
Rodolfo Adrián
• 0
1
vote
1
reply
327
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 days ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
127
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
133
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
2 days ago by
Moinuddin
• 0
0
votes
1
reply
175
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Jacek
▴ 20
0
votes
0
replies
136
views
How can i use ESM-1v ?
VEP
ESM-1v
2 days ago by
Meto
• 0
0
votes
0
replies
149
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Long
• 0
0
votes
0
replies
144
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
3 days ago by
kilcdincer
▴ 10
0
votes
0
replies
163
views
genomic region of transcription factor
search
HOMER
motif
3 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
374
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 3 days ago by
dthorbur
★ 2.0k • written 4 days ago by
BATMAN
• 0
0
votes
6
replies
363
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
3 days ago by
hannes.bongartz
• 0
0
votes
0
replies
147
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 3 days ago by
GenoMax
142k • written 3 days ago by
yura.grabovska
▴ 90
1
vote
1
reply
202
views
constructing pangenome through psvcp
psvcp
pangenome
2 days ago by
analyst
▴ 50
0
votes
4
replies
297
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 7 hours ago by
dthorbur
★ 2.0k • written 3 days ago by
Umer
▴ 50
0
votes
2
replies
252
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
melissachua90
▴ 70
0
votes
0
replies
134
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
3 days ago by
Varsha
• 0
0
votes
1
reply
425
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 3 days ago by
GenoMax
142k • written 3 days ago by
huxiangyulove
• 0
0
votes
0
replies
152
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
4 days ago by
O.rka
▴ 720
0
votes
4
replies
341
views
Merge clusters in Seurat UMAP
seurat
umap
3 days ago by
kilcdincer
▴ 10
0
votes
0
replies
158
views
Use of ichor CNA
Dog
CNA
genome
4 days ago by
sainavyav22
• 0
2
votes
2
replies
278
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 4 days ago by
Ram
43k • written 4 days ago by
txema.heredia
▴ 130
0
votes
0
replies
160
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
4 days ago by
Jsarria.EEAD
• 0
0
votes
2
replies
247
views
How can I calculate the OS of each patient?
overall-survival
6 hours ago by
Pedro
• 0
0
votes
0
replies
153
views
cat-bgen fail
bgenix
updated 4 days ago by
Ram
43k • written 4 days ago by
lambard
• 0
1
vote
1
reply
205
views
API kegg - IndexError: list index out of range
kegg
API
updated 3 days ago by
Nyksubuz
▴ 20 • written 4 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
144
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
4 days ago by
ebertomeup
• 0
0
votes
3
replies
284
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
0
votes
0
replies
149
views
select set of intervals that cover a genomic region
GRanges
bed
4 days ago by
ntsopoul
▴ 60
0
votes
2
replies
214
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
22 hours ago by
Luqman
• 0
0
votes
5
replies
319
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
2 hours ago by
mavy
▴ 10
0
votes
1
reply
178
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 4 days ago by
Michael
54k • written 5 days ago by
mgranada3
▴ 30
0
votes
1
reply
157
views
Add line under stat test
stats
R
updated 3 days ago by
Nyksubuz
▴ 20 • written 5 days ago by
Ghada
• 0
319 results • Page
1 of 7
Recent Votes
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
A: Bcftools merge taking too much time and producing large file
Answer: Kraken2 database
A: Why gene expression data should be log2 transformed?
Answer: Filter Genome for Specific Sites
Answer: Filter Genome for Specific Sites
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Recent Awards •
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Scholar
to
GenoMax
142k
Popular Question
to
tothepoint
▴ 800
Popular Question
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safeassli
▴ 10
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curious
▴ 750
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manaswwm
▴ 510
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Raghad
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Pierre Lindenbaum
161k
Recent Replies
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Hello I have a quick question, I did as you said , and further added the traits, found the correlation among the modules and the traits us…
Comment: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
ojaswinipandey
• 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
Dave Carlson
★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool
by
Ram
43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results
by
GenoMax
142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
Comment: Filter Genome for Specific Sites
by
Anita
• 0
Great, thank you!
Comment: Filter Genome for Specific Sites
by
Anita
• 0
This is unhelpful and doesn't answer my question.
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
It seems that the authors in this paper have used paired-end sequences only for their analysis, and for that, they would also have used the…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
Harshita
• 0
Thank you so much for helping me out in this! I have used most of the sequences that are found in this table. But, some samples like the…
Answer: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
Looks like the samples are from this project: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA320483&o=acc_s%3Aa This table has the SR…
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