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116,986 results • Page
1 of 2340
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Votes
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0
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0
replies
17
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
53 minutes ago by
Ngrin
• 0
0
votes
0
replies
15
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
1 hour ago by
O.rka
▴ 720
4
votes
5
replies
4.3k
views
Tool:
GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly
Structural-Variation
Variant-Calling
updated 1 hour ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
0
replies
18
views
Help! Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
1 hour ago by
BATMAN
• 0
797
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.4 years ago by
Istvan Albert
100k
0
votes
3
replies
125
views
Merge clusters in Seurat UMAP
seurat
umap
updated 1 hour ago by
Ram
43k • written 4 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
42
views
Use of ichor CNA
Dog
CNA
genome
6 hours ago by
sainavyav22
• 0
2
votes
2
replies
126
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 4 hours ago by
Ram
43k • written 7 hours ago by
txema.heredia
▴ 130
0
votes
0
replies
53
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 1 hour ago by
Ram
43k • written 8 hours ago by
carlopecoraro2
★ 2.5k
3
votes
2
replies
151
views
Details on salmon index
Salmon
updated 8 hours ago by
Rob
6.6k • written 15 hours ago by
Lorenzo
• 0
0
votes
0
replies
52
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
8 hours ago by
Jsarria.EEAD
• 0
0
votes
1
reply
101
views
How can I calculate the OS of each patient?
overall-survival
updated 9 hours ago by
ATpoint
82k • written 9 hours ago by
Pedro
• 0
0
votes
1
reply
104
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 9 hours ago by
Ram
43k • written 11 hours ago by
m90
▴ 30
0
votes
0
replies
52
views
cat-bgen fail
bgenix
updated 9 hours ago by
Ram
43k • written 9 hours ago by
lambard
• 0
2
votes
4
replies
226
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
genome
updated 9 hours ago by
Ram
43k • written 16 hours ago by
Ali
• 0
3
votes
3
replies
148
views
getting exon coordinates
genomics
updated 9 hours ago by
Ram
43k • written 11 hours ago by
Xbox_27
• 0
3
votes
5
replies
196
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
updated 1 hour ago by
GenoMax
142k • written 11 hours ago by
Gabriel R.
★ 2.9k
0
votes
3
replies
196
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 hour ago by
Ram
43k • written 1 day ago by
vk
▴ 10
1
vote
5
replies
196
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 1 hour ago by
Ram
43k • written 14 hours ago by
manuelmourato25
• 0
3
votes
4
replies
312
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 11 hours ago by
GenoMax
142k • written 14 hours ago by
Pierre Lindenbaum
161k
1
vote
9
replies
508
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
updated 4 hours ago by
swbarnes2
14k • written 1 day ago by
egascon
• 0
0
votes
0
replies
64
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 hour ago by
Ram
43k • written 15 hours ago by
mirwa.zidi93
• 0
0
votes
0
replies
61
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
16 hours ago by
Novogene
▴ 420
0
votes
0
replies
67
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
17 hours ago by
ebertomeup
• 0
0
votes
1
reply
111
views
Sam file Header problem
Sam
Header
problem
file
updated 17 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
saifulislam99121
• 0
1
vote
4
replies
191
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 1 hour ago by
Ram
43k • written 1 day ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
525
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 20 hours ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
76
views
select set of intervals that cover a genomic region
GRanges
bed
20 hours ago by
ntsopoul
▴ 60
1
vote
1
reply
97
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 1 hour ago by
Ram
43k • written 20 hours ago by
dwpeng
▴ 10
0
votes
0
replies
69
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
22 hours ago by
Luqman
• 0
1
vote
3
replies
172
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 1 hour ago by
Ram
43k • written 22 hours ago by
sooni
▴ 20
0
votes
2
replies
137
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
18 hours ago by
mavy
▴ 10
1
vote
1
reply
195
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 day ago by
ramiro.barrantes
• 0
1
vote
4
replies
279
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
8 hours ago by
diqixiaoyaoer
▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML
ncbi
entrez-direct
updated 1 day ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
129
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 15 hours ago by
Michael
54k • written 1 day ago by
mgranada3
▴ 30
0
votes
0
replies
86
views
Add line under stat test
stats
R
1 day ago by
Ghada
• 0
1
vote
5
replies
771
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
0
votes
0
replies
83
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Rodolfo Adrián
• 0
1
vote
3
replies
174
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 1 day ago by
shpak.max
▴ 50
2
votes
4
replies
242
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 1 day ago by
yura.grabovska
▴ 90 • written 1 day ago by
ev97
▴ 20
1
vote
13
replies
507
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 4 hours ago by
Ram
43k • written 1 day ago by
hophuquy0944
• 0
0
votes
4
replies
214
views
Sequencing Depth (Read Depth) Calculations
depth
22 hours ago by
LucisTheFather
• 0
0
votes
1
reply
122
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
1 day ago by
asalimih
▴ 60
0
votes
0
replies
93
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
1 day ago by
jway
• 0
2
votes
2
replies
166
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 10 hours ago by
Ram
43k • written 1 day ago by
jsmith120f
• 0
2
votes
2
replies
181
views
genome finishing
finishing
genome
updated 1 day ago by
nd48
▴ 20 • written 1 day ago by
trezini
• 0
1
vote
5
replies
206
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
biology_inform
▴ 50
1
vote
4
replies
272
views
Add stats to boxplot in R
stats
R
1 day ago by
Ghada
• 0
0
votes
1
reply
140
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 13 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
116,986 results • Page
1 of 2340
Recent Votes
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
Answer: --normalizeUsing RPGC
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Takuma
▴ 20
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BATMAN
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Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
by
dario.garvan
▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo.
by
Ram
43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP
by
bk11
★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
txema.heredia
▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
swbarnes2
14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty
by
Jordan M Eizenga
▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly
by
sansan_96
▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
e.r.zakiev
▴ 210
Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
Comment: Is there any way to modify this pie chart ?
by
marco.barr
▴ 120
Try following the same logic as the guide which adds the labels about halfway through each pie slice value. Check column's name in script b…
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