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12,354 results • Page
2 of 248
Sort: Rank
Rank
Views
Votes
Replies
1
vote
4
replies
295
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 1 day ago by
Ram
44k • written 1 day ago by
Harshita
• 0
2
votes
4
replies
234
views
Filter Genome for Specific Sites
bedtools
updated 1 day ago by
Ram
44k • written 1 day ago by
Anita
• 0
0
votes
3
replies
243
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 1 day ago by
marco.barr
▴ 130 • written 2 days ago by
Mohamed Samir
▴ 20
1
vote
1
reply
123
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
niruf
• 0
0
votes
0
replies
93
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 1 day ago by
Ram
44k • written 1 day ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
130
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
1 day ago by
Biostar
2.8k
3
votes
5
replies
432
views
Super ehancers
enhancers
updated 18 hours ago by
jared.andrews07
★ 17k • written 20 days ago by
Oburah
• 0
0
votes
2
replies
175
views
vcf phasing
beagle
WhatsHap
phasing
6 hours ago by
safeassli
▴ 10
0
votes
2
replies
204
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
1 day ago by
sainavyav22
• 0
0
votes
1
reply
606
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 1 day ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
189
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 1 day ago by
Ram
44k • written 2 days ago by
Sony
▴ 10
0
votes
3
replies
198
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 1 day ago by
Ram
44k • written 2 days ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
93
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 1 day ago by
Ram
44k • written 2 days ago by
ev97
▴ 20
0
votes
1
reply
138
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 2 days ago by
marco.barr
▴ 130 • written 2 days ago by
sooni
▴ 20
0
votes
1
reply
105
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jinyi
• 0
0
votes
0
replies
83
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
2 days ago by
V_Vibes
• 0
0
votes
0
replies
151
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 1 day ago by
Ram
44k • written 2 days ago by
JorgeVallejo
▴ 20
0
votes
0
replies
101
views
transcriptome annotation
annotation
trinity
transcriptome
updated 1 day ago by
Ram
44k • written 2 days ago by
Asim Bin Arshad
• 0
0
votes
5
replies
225
views
Why most genes have high padj values
RNA-seq
DEG
updated 1 day ago by
Ram
44k • written 2 days ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 2 days ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
146
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 2 days ago by
zx8754
11k • written 2 days ago by
Ali
• 0
0
votes
4
replies
247
views
GO analysis: p-value range
GO
R
updated 2 days ago by
Matthias Zepper
4.6k • written 2 days ago by
sooni
▴ 20
1
vote
2
replies
231
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 1 day ago by
colindaven
6.4k • written 2 days ago by
Dr.
• 0
0
votes
3
replies
240
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 2 days ago by
GenoMax
142k • written 3 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
102
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
2 days ago by
Maryam
• 0
0
votes
4
replies
335
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
2 days ago by
Bibi
• 0
1
vote
2
replies
354
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 2 days ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
113
views
handling bio replicates for chromHMM
replicates
chromHMM
2 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
104
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
2 days ago by
DGTool
▴ 20
1
vote
1
reply
181
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 2 days ago by
ATpoint
82k • written 2 days ago by
rj.rezwan
• 0
0
votes
2
replies
322
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
2 days ago by
Ezequiel
• 0
2
votes
0
replies
190
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
3 days ago by
micah
▴ 30
0
votes
0
replies
120
views
problems in installing rDock
rDock
updated 1 day ago by
Ram
44k • written 3 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 3 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
727
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 3 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
2
replies
381
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 19 hours ago by
finch
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
139
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
147
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
4 days ago by
Moinuddin
• 0
0
votes
1
reply
188
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Jacek
▴ 20
2
votes
1
reply
260
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 3 days ago by
Gordon Smyth
★ 7.2k • written 4 days ago by
marineandriot
• 0
0
votes
0
replies
149
views
How can i use ESM-1v ?
VEP
ESM-1v
4 days ago by
Meto
• 0
0
votes
0
replies
158
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Long
• 0
2
votes
3
replies
338
views
Trimming tool
Trimming
updated 1 day ago by
Ram
44k • written 4 days ago by
GeneC
• 0
0
votes
0
replies
151
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
4 days ago by
kilcdincer
▴ 10
0
votes
2
replies
271
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 4 days ago by
LauferVA
4.2k • written 4 days ago by
ijarne
• 0
0
votes
0
replies
166
views
genomic region of transcription factor
search
HOMER
motif
4 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
392
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 4 days ago by
dthorbur
★ 2.0k • written 5 days ago by
BATMAN
• 0
0
votes
6
replies
383
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
4 days ago by
hannes.bongartz
• 0
0
votes
0
replies
155
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 5 days ago by
GenoMax
142k • written 5 days ago by
yura.grabovska
▴ 90
4
votes
9
replies
643
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 6 days ago by
diqixiaoyaoer
▴ 20
12,354 results • Page
2 of 248
Recent Votes
Construction of circos plot from WGS data
Answer: Different SNP at the at a position in vcf file compared to REF and ALT allele.
Answer: Different SNP at the at a position in vcf file compared to REF and ALT allele.
Different SNP at the at a position in vcf file compared to REF and ALT allele.
Comment: downloading chemical database from ChEMBL
Seurat-Merging and integrate
voom mean-variance plot has set of genes where variance increases with expression level
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Comment: samtools write-index
by
Pierre Lindenbaum
161k
can you please retry, but add rm -vf alignment.sorted.bam.bai before invoking minimap2. And `-o 'alignment.sorted.bam` should be enou…
Answer: from CRAM to fastq
by
Pierre Lindenbaum
161k
if the CRAM/BAM is paire-end, it **must** be sorted on query name using samtools collate https://x.com/lh3lh3/status/1132756684789768202 …
Comment: from CRAM to fastq
by
machaalani29
• 0
one of the issues is that I am not very sure how the sequencing was done, but I think it was single end. any suggestions hoot do that?
Comment: from CRAM to fastq
by
machaalani29
• 0
the option -c is to compress the file
Comment: from CRAM to fastq
by
GenoMax
142k
Possibly. You appear to have written the data to a single file (in case it was paired-end to begin with). Check to make sure secondary alig…
Comment: converting transcript IDs (Ensembl) to gene symbols in R
by
GenoMax
142k
https://www.biostars.org/u/18990/ : Please do not delete threads that have received a comment/answer.
Comment: downloading chemical database from ChEMBL
by
GenoMax
142k
Activities with `cucurbitacin A`: https://www.ebi.ac.uk/chembl/web_components/explore/activities/STATE_ID:RHxG8uDfrtbmiyaY55ic-w%3D%3D `cu…
Comment: KEGG analysis in R
by
letizia.ottaviani
• 0
Hello, I have a problem to do the analysis in R. I want to kindly ask you: How did you perform KEGG pathway enrichment analysis in R for…
Comment: downloading chemical database from ChEMBL
by
s
• 0
Thank you for your reply. I am still struggling with the first step, namely "select a compound" . can you be more specific with this step? …
Comment: No output when converting transcript IDs to gene symbols
by
ATpoint
82k
Honestly, why the overhead with biomart? Get a GTF file that matches your annotations, and just do a left join with your transcript IDs, it…
Answer: vg autoindex seems stuck after a week of running
by
Jouni Sirén
▴ 370
GCSA construction is fragile. It can use effectively unlimited amounts of time, memory, and disk space if the graph is too complex. That's …
Comment: Blastn, need help to increase speed
by
Dunois
★ 2.5k
What databases are you using that are creating such large index files?
Answer: Kraken2 Custom Database non-deterministic results
by
colindaven
6.4k
You're using 2 different databases, so results are obviously different. This has nothing to do with deterministic or stochastic behaviour. …
Answer: How to get 2 seurat objects into a DEseq
by
ultraanfibio
▴ 30
Its probably best practice to read all samples into the same seurat object, then do the clustering and asign the cell type labels. Anyways …
Comment: How do we do quantification using stringtie merge option for all the merged samp
by
ATpoint
82k
I ask the same I always ask when people use stringtie for human data. Do you really need a transcript assembly or do you just want gene cou…
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