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88 results • Page
1 of 2
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
12
views
transcriptome annotation
annotation
transcriptome
cone
trinity
snails
conus
genome
25 minutes ago by
Asim Bin Arshad
• 0
0
votes
3
replies
38
views
Why most genes have high padj values
deg
padj
bulkRNA
updated 36 minutes ago by
ATpoint
82k • written 1 hour ago by
mnx0723
• 0
0
votes
1
reply
34
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
identical
sequences.
updated 1 hour ago by
Pierre Lindenbaum
161k • written 1 hour ago by
Sony
▴ 10
0
votes
1
reply
46
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 1 hour ago by
ATpoint
82k • written 3 hours ago by
Pegasus
▴ 100
0
votes
0
replies
44
views
Error in using BioSampleParser tool: subscript out of bounds
R
6 hours ago by
Mohamed Samir
▴ 20
0
votes
1
reply
63
views
GO analysis: p-value range
GO
R
updated 1 hour ago by
marco.barr
▴ 130 • written 8 hours ago by
sooni
▴ 20
0
votes
0
replies
56
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
10 hours ago by
Maryam
• 0
0
votes
4
replies
270
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
10 hours ago by
Bibi
• 0
0
votes
0
replies
71
views
handling bio replicates for chromHMM
replicates
chromHMM
14 hours ago by
Hasan_Daaboul
• 0
0
votes
0
replies
62
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
15 hours ago by
DGTool
▴ 20
0
votes
0
replies
83
views
problems in installing rDock
rDock
make
Installation
Error
1 day ago by
Rodolfo Adrián
• 0
1
vote
1
reply
301
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 1 day ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
105
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Mohamed Samir
▴ 20
0
votes
0
replies
109
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
1 day ago by
Moinuddin
• 0
0
votes
1
reply
150
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Jacek
▴ 20
0
votes
0
replies
118
views
How can i use ESM-1v ?
VEP
ESM-1v
2 days ago by
Meto
• 0
0
votes
0
replies
125
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Long
• 0
0
votes
0
replies
122
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
146
views
genomic region of transcription factor
search
HOMER
motif
2 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
356
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 2 days ago by
dthorbur
★ 2.0k • written 3 days ago by
BATMAN
• 0
0
votes
6
replies
345
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
2 days ago by
hannes.bongartz
• 0
0
votes
0
replies
129
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 2 days ago by
GenoMax
142k • written 2 days ago by
yura.grabovska
▴ 90
1
vote
1
reply
188
views
constructing pangenome through psvcp
psvcp
pangenome
1 day ago by
analyst
▴ 50
0
votes
3
replies
246
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 2 hours ago by
nd48
▴ 20 • written 2 days ago by
Umer
▴ 50
0
votes
2
replies
243
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
129
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
398
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 2 days ago by
GenoMax
142k • written 3 days ago by
huxiangyulove
• 0
0
votes
0
replies
148
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
3 days ago by
O.rka
▴ 720
0
votes
4
replies
336
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
158
views
Use of ichor CNA
Dog
CNA
genome
3 days ago by
sainavyav22
• 0
2
votes
2
replies
275
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 days ago by
Ram
43k • written 3 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
3 days ago by
Jsarria.EEAD
• 0
0
votes
1
reply
213
views
How can I calculate the OS of each patient?
overall-survival
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Pedro
• 0
0
votes
0
replies
152
views
cat-bgen fail
bgenix
updated 3 days ago by
Ram
43k • written 3 days ago by
lambard
• 0
1
vote
1
reply
201
views
API kegg - IndexError: list index out of range
kegg
API
updated 3 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
141
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
4 days ago by
ebertomeup
• 0
0
votes
3
replies
280
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
147
views
select set of intervals that cover a genomic region
GRanges
bed
4 days ago by
ntsopoul
▴ 60
0
votes
2
replies
208
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
6 hours ago by
Luqman
• 0
0
votes
4
replies
285
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
1
reply
177
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 3 days ago by
Michael
54k • written 4 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 4 days ago by
Ghada
• 0
0
votes
0
replies
114
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Rodolfo Adrián
• 0
1
vote
16
replies
751
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 day ago by
GenoMax
142k • written 4 days ago by
hophuquy0944
• 0
0
votes
1
reply
141
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
4 days ago by
asalimih
▴ 60
0
votes
0
replies
111
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
4 days ago by
jway
• 0
0
votes
1
reply
155
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 3 days ago by
Papyrus
★ 2.9k • written 4 days ago by
yura.grabovska
▴ 90
0
votes
1
reply
153
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Lélé
▴ 10
0
votes
3
replies
172
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
4 days ago by
Esraa
• 0
0
votes
0
replies
99
views
ReactomeGSA
ReactomeGSA
4 days ago by
Shaimaa Gamal
▴ 10
88 results • Page
1 of 2
Recent Votes
Answer: How to find tandem duplications pattern in a DNA sequence
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
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Recent Replies
Comment: Why most genes have high padj values
by
ATpoint
82k
788 differential genes is a lot. What is the problem?
Comment: Why most genes have high padj values
by
mnx0723
• 0
Sorry, I made edits.
Comment: Why most genes have high padj values
by
Pierre Lindenbaum
161k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
Try adding: `scale_y_continuous(breaks=seq(0, max_count, by=0.05))`
Comment: Functional enrichment analysis for unique gene IDs
by
ATpoint
82k
If these genes do not have a symbol then it is utterly unlikely that anyone has looked at their function. I would get their Ensembl IDs and…
Comment: Add stats to the plot
by
marco.barr
▴ 130
The error is likely due to the fact that the structure of your data in data4.ts and data2.ts may not contain the Condition values. The grou…
Comment: How to find identical sequences in genome fasta file (by Python or any possible
by
Pierre Lindenbaum
161k
+ https://www.biostars.org/p/3003/ + https://www.biostars.org/p/9550118/ + https://www.biostars.org/p/158148/
Answer: How to find tandem duplications pattern in a DNA sequence
by
micah
▴ 30
I built a web application can directly find repeat unit and repeat times, try it at http://64.64.240.35:8050/. ![Dot plot][1] ![5 tandem …
Comment: What marks a De-Novo Genome assembly as FAILED?
by
nd48
▴ 20
I would urge you to consider different approaches for benchmarking before deciding on one. In particular, I found that assembling long read…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed
by
m13113153781
• 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
KHURRAM SHAHZAD
• 0
Thank you it works
Answer: Add stats to the plot
by
Ghada
• 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
Bibi
• 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot
by
GenoMax
142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
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