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117,028 results • Page
2 of 2341
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Votes
Replies
0
votes
0
replies
134
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
410
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 3 days ago by
GenoMax
142k • written 3 days ago by
huxiangyulove
• 0
0
votes
0
replies
151
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
3 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 3 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
339
views
Merge clusters in Seurat UMAP
seurat
umap
3 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
1
vote
0
replies
167
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 3 days ago by
Ram
43k • written 3 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
354
views
Details on salmon index
Salmon
updated 3 days ago by
Rob
6.6k • written 4 days ago by
Lorenzo
• 0
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
1
vote
1
reply
218
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 3 days ago by
Ram
43k • written 4 days ago by
m90
▴ 30
0
votes
0
replies
152
views
cat-bgen fail
bgenix
updated 3 days ago by
Ram
43k • written 3 days ago by
lambard
• 0
3
votes
4
replies
339
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 2 days ago by
Jeremy Leipzig
22k • written 4 days ago by
Ali
• 0
3
votes
3
replies
251
views
getting exon coordinates
genomics
updated 3 days ago by
Ram
43k • written 4 days ago by
Xbox_27
• 0
0
votes
4
replies
332
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 3 days ago by
Tony
• 0 • written 4 days ago by
vk
▴ 10
1
vote
5
replies
318
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 3 days ago by
Ram
43k • written 4 days ago by
manuelmourato25
• 0
3
votes
4
replies
414
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Pierre Lindenbaum
161k
2
votes
11
replies
734
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
3 days ago by
egascon
• 0
1
vote
1
reply
202
views
API kegg - IndexError: list index out of range
kegg
API
updated 3 days ago by
Nyksubuz
▴ 20 • written 4 days ago by
mirwa.zidi93
• 0
0
votes
0
replies
145
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
4 days ago by
Novogene
▴ 420
0
votes
0
replies
142
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
4 days ago by
ebertomeup
• 0
0
votes
3
replies
281
views
Sam file Header problem
Sam
Header
problem
file
updated 3 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
saifulislam99121
• 0
1
vote
3
replies
286
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 3 days ago by
Ram
43k • written 5 days ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
594
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 4 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
0
replies
147
views
select set of intervals that cover a genomic region
GRanges
bed
4 days ago by
ntsopoul
▴ 60
1
vote
1
reply
197
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 3 days ago by
Ram
43k • written 4 days ago by
dwpeng
▴ 10
0
votes
2
replies
212
views
BiomartException: Query ERROR for existing dataset in BioMart
biomart
ensembl
wheat
python
pybiomart
11 hours ago by
Luqman
• 0
2
votes
3
replies
258
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 3 days ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
4
replies
286
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
2 days ago by
mavy
▴ 10
1
vote
1
reply
249
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
4 days ago by
ramiro.barrantes
• 0
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 4 days ago by
Ram
43k • written 3.9 years ago by
millere
• 0
0
votes
1
reply
178
views
What's next after GATK variant calling pipeline?
GATK
pipeline
figures
DNA-seq
updated 4 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
1
vote
5
replies
808
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
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
3
replies
209
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 4 days ago by
shpak.max
▴ 50
2
votes
4
replies
277
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 4 days ago by
yura.grabovska
▴ 90 • written 4 days ago by
ev97
▴ 20
1
vote
16
replies
753
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
4
replies
248
views
Sequencing Depth (Read Depth) Calculations
depth
4 days ago by
LucisTheFather
• 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
2
votes
2
replies
193
views
Cannot install bwa-mem2 via conda
conda
mamba
python
updated 3 days ago by
Ram
43k • written 4 days ago by
jsmith120f
• 0
2
votes
2
replies
206
views
genome finishing
finishing
genome
updated 4 days ago by
nd48
▴ 20 • written 5 days ago by
trezini
• 0
1
vote
5
replies
231
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
biology_inform
▴ 50
1
vote
4
replies
300
views
Add stats to boxplot in R
stats
R
4 days ago by
Ghada
• 0
0
votes
1
reply
157
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 4 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
5
replies
312
views
calculating genomic coverage/ base overlap in R
genomics
updated 2 days ago by
1769mkc
★ 1.2k • written 5 days ago by
Xbox_27
• 0
1
vote
5
replies
273
views
Annotating file using bcftools
annotation
plink
bcftools
3 days ago by
kl
▴ 10
117,028 results • Page
2 of 2341
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Answer: Ti Tv ratio and their usefulness in exome sequencing
Answer: Ti Tv ratio and their usefulness in exome sequencing
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Answer: How do you generate TMM normalized counts using EdgeR?
Analysing Microarray Data In Bioconductor
Answer: Q: GenomeScope input and how to interpret the results
Answer: How to find tandem duplications pattern in a DNA sequence
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Answer: How to find identical sequences in genome fasta file (by Python or any possible
by
GenoMax
142k
> My final purpose are find and remove any identical sequences present in my genome fasta file. You can use `clumpify.sh` from BBMap suite…
Comment: GO analysis: Indicate genes corresponding to the pathway
by
marco.barr
▴ 130
I think you have set a filter to get these pahways upstream from the DEG results. You should extract the IDs or names of the genes that you…
Comment: GATK Structural Variants Pipeline - Steps
by
Bioinformatics_begginner
▴ 20
Thank you for the response, I mean those tools aren't all the steps from fasta to vcf. Would be key understanding the aligner, reference us…
Comment: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Answer: GATK Structural Variants Pipeline - Steps
by
Pierre Lindenbaum
161k
> A structural variation pipeline for short-read sequencing https://github.com/broadinstitute/gatk-sv
Comment: GATK Structural Variants Pipeline - Steps
by
DGTool
▴ 20
If it is just the tools that they used which you are looking for, the first link in the overview section of that page leads to the followin…
Comment: GO analysis: p-value range
by
Matthias Zepper
4.6k
It is just a warning that you add a new scale to a ggplot2 plot, that already has an existing one, which will get replaced. Nothing to worr…
Comment: GO analysis: p-value range
by
marco.barr
▴ 130
If you write me the code you used I can help you more
Comment: GO analysis: p-value range
by
sooni
▴ 20
When I run the code, the following message appears: Scale for y is already present. Adding another scale for y, which will replace…
Comment: Why most genes have high padj values
by
mnx0723
• 0
In the case of other samples, the total number of genes is at least 3,000 more than that one, but it seems to be a relatively small number.…
Comment: How to hide label in layout file of MCscan (python version)
by
jinyi
• 0
Command line is as follows: python -m jcvi.graphics.synteny Cs.Cm.i1.blocks Cs_Cm.bed layout2.txt
Comment: Add stats to the plot
by
marco.barr
▴ 130
Thank you, it seems to be clearer. Your Condition already has two factorial levels. You can replace these names in groups 1 and 2. da…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi, I also had the same problem. If you check its github page there have been no releases for many years and these errors cannot be fixed. …
Comment: Add stats to the plot
by
Ghada
• 0
Thanks, thats really helpful ![enter image description here][1] ![enter image description here][2] [1]: /media/images/0470f3dc-5945-…
Comment: PCA Visualization error in R
by
marco.barr
▴ 130
SNPRelate is an R package that is able to read from VCF files directly and perform PCA and IBD/IBS. See the documentation for details in Bi…
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