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117,008 results • Page
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Votes
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0
votes
0
replies
5
views
Add stats to the plot
plotting
stats
R
2 minutes ago by
Ghada
• 0
0
votes
0
replies
9
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
28 minutes ago by
micah
• 0
0
votes
0
replies
31
views
problems in installing rDock
rDock
make
Installation
Error
3 hours ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 4 hours ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
0
votes
0
replies
26
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
4 hours ago by
KHURRAM SHAHZAD
• 0
798
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
1
vote
2
replies
632
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 6 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
1
reply
263
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 11 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
0
votes
0
replies
71
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 17 hours ago by
Pierre Lindenbaum
161k • written 17 hours ago by
Mohamed Samir
▴ 20
0
votes
0
replies
79
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
20 hours ago by
Moinuddin
• 0
0
votes
1
reply
112
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
Jacek
▴ 20
2
votes
1
reply
181
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 10 hours ago by
Gordon Smyth
★ 7.2k • written 1 day ago by
marineandriot
• 0
0
votes
0
replies
90
views
How can i use ESM-1v ?
VEP
ESM-1v
1 day ago by
Meto
• 0
0
votes
1
reply
182
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
Ezequiel
• 0
0
votes
0
replies
97
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
2
replies
198
views
Trimming tool
Trimmer
tool
updated 1 day ago by
ntsopoul
▴ 60 • written 1 day ago by
GeneC
• 0
0
votes
0
replies
93
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
1 day ago by
kilcdincer
▴ 10
0
votes
2
replies
198
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 1 day ago by
LauferVA
4.2k • written 1 day ago by
ijarne
• 0
0
votes
0
replies
119
views
genomic region of transcription factor
search
HOMER
motif
1 day ago by
qudrat.nii
▴ 10
1
vote
5
replies
328
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
0
votes
6
replies
306
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
0
votes
0
replies
101
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 1 day ago by
GenoMax
142k • written 1 day ago by
yura.grabovska
▴ 90
4
votes
7
replies
488
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 1 day ago by
marco.barr
▴ 130 • written 3 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
154
views
constructing pangenome through psvcp
psvcp
pangenome
18 hours ago by
analyst
▴ 50
0
votes
1
reply
149
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
Umer
▴ 50
0
votes
4
replies
304
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 1 day ago by
txema.heredia
▴ 130 • written 2 days ago by
Ngrin
• 0
4
votes
9
replies
451
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
1 day ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
213
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
0
votes
0
replies
103
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
2 days ago by
Varsha
• 0
0
votes
1
reply
316
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 1 day ago by
GenoMax
142k • written 2 days ago by
huxiangyulove
• 0
0
votes
0
replies
121
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
2 days ago by
O.rka
▴ 720
4
votes
5
replies
4.4k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 2 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
305
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
0
replies
130
views
Use of ichor CNA
Dog
CNA
genome
2 days ago by
sainavyav22
• 0
2
votes
2
replies
245
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 2 days ago by
Ram
43k • written 2 days ago by
txema.heredia
▴ 130
1
vote
0
replies
139
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
323
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 3 days ago by
Lorenzo
• 0
0
votes
0
replies
133
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
2 days ago by
Jsarria.EEAD
• 0
0
votes
1
reply
185
views
How can I calculate the OS of each patient?
overall-survival
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Pedro
• 0
1
vote
1
reply
193
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
m90
▴ 30
0
votes
0
replies
132
views
cat-bgen fail
bgenix
updated 2 days ago by
Ram
43k • written 2 days ago by
lambard
• 0
3
votes
4
replies
313
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 1 day ago by
Jeremy Leipzig
22k • written 3 days ago by
Ali
• 0
3
votes
3
replies
232
views
getting exon coordinates
genomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
0
votes
4
replies
310
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 2 days ago by
Tony
• 0 • written 3 days ago by
vk
▴ 10
1
vote
5
replies
297
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 2 days ago by
Ram
43k • written 2 days ago by
manuelmourato25
• 0
3
votes
4
replies
396
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 2 days ago by
GenoMax
142k • written 3 days ago by
Pierre Lindenbaum
161k
2
votes
11
replies
705
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
2 days ago by
egascon
• 0
1
vote
1
reply
188
views
API kegg - IndexError: list index out of range
kegg
API
updated 2 days ago by
Nyksubuz
▴ 20 • written 3 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
135
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
3 days ago by
Novogene
▴ 420
0
votes
0
replies
138
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
3 days ago by
ebertomeup
• 0
117,008 results • Page
1 of 2341
Recent Votes
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?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Recent Replies
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
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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