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84 results • Page
2 of 2
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0
votes
4
replies
310
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
1
reply
330
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 2 days ago by
huxiangyulove
• 0
0
votes
1
reply
155
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 2 days ago by
dthorbur
★ 2.0k • written 2 days ago by
Umer
▴ 50
0
votes
0
replies
106
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
0
votes
0
replies
124
views
genomic region of transcription factor
search
HOMER
motif
1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
100
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
1 day ago by
kilcdincer
▴ 10
0
votes
6
replies
313
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
0
votes
0
replies
102
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Long
• 0
0
votes
0
replies
97
views
How can i use ESM-1v ?
VEP
ESM-1v
1 day ago by
Meto
• 0
0
votes
4
replies
282
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
2
replies
311
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
0
votes
0
replies
85
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
1 day ago by
Moinuddin
• 0
0
votes
0
replies
79
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 21 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
Mohamed Samir
▴ 20
0
votes
2
replies
299
views
Traveler with Infernal mapping failed
r2dt
updated 16 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
0
votes
0
replies
49
views
problems in installing rDock
rDock
make
Installation
Error
7 hours ago by
Rodolfo Adrián
• 0
0
votes
0
replies
34
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
2 hours ago by
Bibi
• 0
0
votes
1
reply
56
views
Add stats to the plot
R
stats
plotting
updated 1 hour ago by
GenoMax
142k • written 4 hours ago by
Ghada
• 0
0
votes
1
reply
122
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
112
views
lncRNA
tcga
lncrna
6 days ago by
jain72744
▴ 10
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
6 days ago by
analyst
▴ 50
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
6 days ago by
beginner123
• 0
0
votes
2
replies
213
views
Output file of samtools flagstat empty
samtools-flagstat
updated 6 days ago by
colindaven
6.4k • written 7 days ago by
ramendra.sarma
• 0
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
6 days ago by
gernophil
▴ 80
0
votes
0
replies
89
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
6 days ago by
JACKY
▴ 140
0
votes
5
replies
326
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by
SilhouetteQ
• 0
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
6 days ago by
atariw
▴ 10
0
votes
1
reply
165
views
consensus sequence calling
consensus
updated 5 days ago by
bk11
★ 2.5k • written 6 days ago by
Ghada
• 0
0
votes
0
replies
105
views
reference-free assembly error assessment tools
assembly
5 days ago by
lagartija
▴ 160
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 5 days ago by
Ram
43k • written 5 days ago by
eking28
• 0
0
votes
0
replies
126
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 5 days ago by
Ram
43k • written 20 days ago by
atharvakarkare14
▴ 40
0
votes
1
reply
162
views
How to process Bulk WES data?
WES
WGS
updated 5 days ago by
GenoMax
142k • written 5 days ago by
wyuan37
• 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 5 days ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 5 days ago by
GenoMax
142k • written 5 days ago by
cedric.blais
• 0
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
5 days ago by
Emily
▴ 20
84 results • Page
2 of 2
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Popular Question
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carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
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Muhammad
• 0
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synat.keam
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Recent Replies
Answer: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
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