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736 results • Page
1 of 15
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0
votes
0
replies
20
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
1 hour ago by
Moinuddin
• 0
0
votes
1
reply
43
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 3 hours ago by
ATpoint
82k • written 3 hours ago by
Jacek
▴ 20
1
vote
1
reply
112
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 2 hours ago by
Gordon Smyth
★ 7.2k • written 17 hours ago by
marineandriot
• 0
0
votes
0
replies
54
views
How can i use ESM-1v ?
VEP
ESM-1v
13 hours ago by
Meto
• 0
0
votes
1
reply
138
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
updated 17 hours ago by
swbarnes2
14k • written 21 hours ago by
Ezequiel
• 0
0
votes
0
replies
69
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 17 hours ago by
GenoMax
142k • written 17 hours ago by
Long
• 0
0
votes
2
replies
167
views
Trimming tool
Trimmer
tool
updated 19 hours ago by
ntsopoul
▴ 60 • written 21 hours ago by
GeneC
• 0
0
votes
0
replies
69
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
20 hours ago by
kilcdincer
▴ 10
0
votes
2
replies
158
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 17 hours ago by
LauferVA
4.2k • written 22 hours ago by
ijarne
• 0
0
votes
0
replies
92
views
genomic region of transcription factor
search
HOMER
motif
22 hours ago by
qudrat.nii
▴ 10
1
vote
5
replies
301
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 22 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
0
votes
6
replies
272
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
17 hours ago by
hannes.bongartz
• 0
0
votes
0
replies
80
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
464
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 2 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
96
views
constructing pangenome through psvcp
psvcp
pangenome
10 minutes ago by
analyst
▴ 50
0
votes
1
reply
123
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
updated 1 day ago by
dthorbur
★ 2.0k • written 1 day ago by
Umer
▴ 50
0
votes
4
replies
264
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 6 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
4
votes
9
replies
427
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
193
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
melissachua90
▴ 70
0
votes
0
replies
82
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
1 day ago by
Varsha
• 0
0
votes
1
reply
247
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 1 day ago by
huxiangyulove
• 0
0
votes
0
replies
101
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
1 day 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 1 day ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
280
views
Merge clusters in Seurat UMAP
seurat
umap
1 day ago by
kilcdincer
▴ 10
0
votes
0
replies
106
views
Use of ichor CNA
Dog
CNA
genome
1 day ago by
sainavyav22
• 0
2
votes
2
replies
221
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 1 day ago by
Ram
43k • written 1 day ago by
txema.heredia
▴ 130
1
vote
0
replies
117
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
299
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
0
votes
0
replies
111
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
1 day ago by
Jsarria.EEAD
• 0
0
votes
1
reply
162
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
171
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
109
views
cat-bgen fail
bgenix
updated 2 days ago by
Ram
43k • written 2 days ago by
lambard
• 0
3
votes
4
replies
289
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 2 days ago by
Ali
• 0
3
votes
3
replies
209
views
getting exon coordinates
genomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
0
votes
4
replies
284
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
1
vote
5
replies
269
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 1 day ago by
Ram
43k • written 2 days ago by
manuelmourato25
• 0
3
votes
4
replies
372
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 2 days ago by
Pierre Lindenbaum
161k
2
votes
11
replies
677
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
1 day ago by
egascon
• 0
1
vote
1
reply
166
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
112
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
2 days ago by
Novogene
▴ 420
0
votes
0
replies
116
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
3
replies
255
views
Sam file Header problem
Sam
Header
problem
file
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
1
vote
3
replies
256
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 1 day ago by
Ram
43k • written 3 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
578
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 2 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
130
views
select set of intervals that cover a genomic region
GRanges
bed
2 days ago by
ntsopoul
▴ 60
1
vote
1
reply
178
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 1 day ago by
Ram
43k • written 2 days ago by
dwpeng
▴ 10
0
votes
1
reply
158
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
Luqman
• 0
2
votes
3
replies
242
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 1 day ago by
Ram
43k • written 2 days ago by
sooni
▴ 20
0
votes
4
replies
264
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
6 hours ago by
mavy
▴ 10
1
vote
1
reply
247
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 0
736 results • Page
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Recent Votes
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?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
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syedahamdani94
• 0
Popular Question
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mohammadhassanj
▴ 260
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dsull
★ 6.0k
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finswimmer
16k
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Ezequiel
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alanh
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Recent Replies
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 precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
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…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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