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188 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
1
vote
3
replies
275
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 2 days ago by
GenoMax
142k • written 5 days ago by
ohtang7
▴ 40
1
vote
2
replies
212
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
mbrav005
• 0
1
vote
2
replies
231
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
1
vote
1
reply
197
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
m90
▴ 30
1
vote
1
reply
148
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 4 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
1
vote
4
replies
346
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 5 days ago by
Ram
43k • written 10 days ago by
samRayne
• 0
1
vote
1
reply
267
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 13 hours ago by
nguyenn6
• 0 • written 12 weeks ago by
star
▴ 10
1
vote
5
replies
329
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
1
vote
1
reply
249
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
3 days ago by
ramiro.barrantes
• 0
1
vote
5
replies
268
views
Annotating file using bcftools
annotation
plink
bcftools
2 days ago by
kl
▴ 10
1
vote
2
replies
1.3k
views
Extracting named fasta sequences according to list with Biopython
Biopython
FASTA
updated 5 days ago by
Rubayetul
• 0 • written 2.6 years ago by
lachiemck
• 0
1
vote
2
replies
635
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 7 hours ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
5 days ago by
Lukas
• 0
1
vote
1
reply
176
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Pegasus
▴ 100
1
vote
4
replies
296
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
3 days ago by
Arton
▴ 10
1
vote
6
replies
1.4k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 5 hours ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
8
replies
455
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 1 day ago by
Alex Reynolds
35k • written 5 days ago by
ntsopoul
▴ 60
1
vote
5
replies
223
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
biology_inform
▴ 50
1
vote
2
replies
184
views
Duplicated sequence samtools
bowtie2
samtools
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Moinuddin
• 0
1
vote
4
replies
318
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 23 hours ago by
Joe
21k • written 10 days ago by
cput
• 0
1
vote
3
replies
290
views
Using ggplotly in R
ggplot
ggplotly
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
jen
▴ 10
1
vote
5
replies
299
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 2 days ago by
Ram
43k • written 3 days ago by
manuelmourato25
• 0
1
vote
1
reply
195
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 2 days ago by
Ram
43k • written 3 days ago by
dwpeng
▴ 10
1
vote
3
replies
279
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 2 days ago by
Ram
43k • written 3 days ago by
kuttibiotech2009
▴ 30
1
vote
3
replies
208
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
shpak.max
▴ 50
1
vote
0
replies
142
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
1
vote
3
replies
445
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
5 days ago by
kalavattam
▴ 190
1
vote
1
reply
190
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
1
vote
1
reply
191
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 2 days ago by
Jordan M Eizenga
▴ 460 • written 13 days ago by
sarumonsus
▴ 10
1
vote
16
replies
734
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 20 hours ago by
GenoMax
142k • written 3 days ago by
hophuquy0944
• 0
1
vote
2
replies
233
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
3 days ago by
MarcosCosta
• 0
1
vote
4
replies
352
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 5 days ago by
Vijith
▴ 30
1
vote
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 0
1
vote
1
reply
157
views
constructing pangenome through psvcp
psvcp
pangenome
20 hours ago by
analyst
▴ 50
1
vote
0
replies
99
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
6 days ago by
tomas4482
▴ 400
0
votes
0
replies
96
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
1 day ago by
kilcdincer
▴ 10
0
votes
2
replies
199
views
Trimming tool
Trimmer
tool
updated 1 day ago by
ntsopoul
▴ 60 • written 1 day ago by
GeneC
• 0
0
votes
6
replies
308
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
0
votes
2
replies
201
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
98
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
1
reply
184
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
93
views
How can i use ESM-1v ?
VEP
ESM-1v
1 day ago by
Meto
• 0
0
votes
7
replies
4.3k
views
B allele frequency (BAF)
snp
updated 1 day ago by
aidangcruickshank
▴ 10 • written 3.7 years ago by
rthapa
▴ 90
0
votes
4
replies
281
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
1 day ago by
mavy
▴ 10
0
votes
4
replies
306
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
0
votes
1
reply
115
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 23 hours ago by
ATpoint
82k • written 23 hours ago by
Jacek
▴ 20
0
votes
5
replies
298
views
calculating genomic coverage/ base overlap in R
genomics
updated 22 hours ago by
1769mkc
★ 1.2k • written 3 days ago by
Xbox_27
• 0
0
votes
0
replies
81
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
21 hours ago by
Moinuddin
• 0
0
votes
0
replies
73
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 18 hours ago by
Pierre Lindenbaum
161k • written 18 hours ago by
Mohamed Samir
▴ 20
0
votes
2
replies
296
views
Traveler with Infernal mapping failed
r2dt
updated 13 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
188 results • Page
2 of 4
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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Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
to
Muhammad
• 0
Popular Question
to
synat.keam
▴ 100
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★ 1.8k
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mohammadhassanj
▴ 260
Recent Replies
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
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.
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