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180 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
100
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
1 day ago by
Maryam
• 0
1
vote
8
replies
443
views
Add stats to the plot
R
updated 8 hours ago by
marco.barr
▴ 130 • written 2 days ago by
Ghada
• 0
0
votes
4
replies
328
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
1
vote
2
replies
351
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 1 day ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
111
views
handling bio replicates for chromHMM
replicates
chromHMM
1 day ago by
Hasan_Daaboul
• 0
0
votes
0
replies
102
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
1 day ago by
DGTool
▴ 20
0
votes
1
reply
166
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 1 day ago by
ATpoint
82k • written 2 days ago by
rj.rezwan
• 0
0
votes
2
replies
315
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
187
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
2 days ago by
micah
▴ 30
0
votes
0
replies
117
views
problems in installing rDock
rDock
updated 20 hours ago by
Ram
44k • written 2 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 2 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
724
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 2 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
1
reply
344
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 days ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
136
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
144
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
3 days ago by
Moinuddin
• 0
0
votes
1
reply
186
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Jacek
▴ 20
2
votes
1
reply
255
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 2 days ago by
Gordon Smyth
★ 7.2k • written 3 days ago by
marineandriot
• 0
0
votes
0
replies
144
views
How can i use ESM-1v ?
VEP
ESM-1v
3 days ago by
Meto
• 0
0
votes
0
replies
156
views
Cell type annotation mixed with other type cells
cell
annotation.
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Long
• 0
2
votes
3
replies
325
views
Trimming tool
Trimming
updated 20 hours ago by
Ram
44k • written 3 days ago by
GeneC
• 0
0
votes
0
replies
148
views
sci-RNA-seq
cell
single
seurat
sci-rna-seq
counts
3 days ago by
kilcdincer
▴ 10
0
votes
2
replies
266
views
GG Sankey plot
GO
sankey_plot
gglpot
updated 3 days ago by
LauferVA
4.2k • written 3 days ago by
ijarne
• 0
0
votes
0
replies
163
views
genomic region of transcription factor
search
HOMER
motif
3 days ago by
qudrat.nii
▴ 10
1
vote
5
replies
378
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 3 days ago by
dthorbur
★ 2.0k • written 4 days ago by
BATMAN
• 0
0
votes
6
replies
367
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
3 days ago by
hannes.bongartz
• 0
0
votes
0
replies
149
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 4 days ago by
GenoMax
142k • written 4 days ago by
yura.grabovska
▴ 90
4
votes
9
replies
624
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 6 hours ago by
marco.barr
▴ 130 • written 5 days ago by
diqixiaoyaoer
▴ 20
1
vote
1
reply
204
views
constructing pangenome through psvcp
psvcp
pangenome
3 days ago by
analyst
▴ 50
1
vote
6
replies
350
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
4 hours ago by
Umer
▴ 50
0
votes
4
replies
360
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 3 days ago by
txema.heredia
▴ 130 • written 4 days ago by
Ngrin
• 0
4
votes
9
replies
503
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
4 days ago by
Gabriel R.
★ 2.9k
0
votes
2
replies
257
views
How to generate table_annovar from VCF input?
vcf
annovar
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
melissachua90
▴ 70
0
votes
0
replies
136
views
How do I quantify the non-coding transcripts that I have generated after using CPAT,PLEK, and BLAST altogether?
transcript
Quantify
non-coding
4 days ago by
Varsha
• 0
0
votes
1
reply
448
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 4 days ago by
GenoMax
142k • written 4 days ago by
huxiangyulove
• 0
0
votes
0
replies
153
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
4 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 4 days ago by
dario.garvan
▴ 520 • written 7.2 years ago by
d-cameron
★ 2.9k
0
votes
4
replies
352
views
Merge clusters in Seurat UMAP
seurat
umap
4 days ago by
kilcdincer
▴ 10
0
votes
0
replies
159
views
Use of ichor CNA
Dog
CNA
genome
4 days ago by
sainavyav22
• 0
2
votes
2
replies
286
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 4 days ago by
Ram
44k • written 4 days ago by
txema.heredia
▴ 130
1
vote
0
replies
169
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 4 days ago by
Ram
44k • written 4 days ago by
carlopecoraro2
★ 2.5k
6
votes
4
replies
365
views
Details on salmon index
Salmon
updated 4 days ago by
Rob
6.6k • written 5 days ago by
Lorenzo
• 0
0
votes
0
replies
163
views
Error when running create-maf-vcf at convertGVCFToHVCFForChrom step - PHGv2
PHG
pangenome
PHG_v2
5 days ago by
Jsarria.EEAD
• 0
0
votes
2
replies
266
views
How can I calculate the OS of each patient?
overall-survival
21 hours ago by
Pedro
• 0
1
vote
1
reply
223
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 5 days ago by
Ram
44k • written 5 days ago by
m90
▴ 30
0
votes
0
replies
155
views
cat-bgen fail
bgenix
updated 5 days ago by
Ram
44k • written 5 days ago by
lambard
• 0
3
votes
4
replies
348
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 4 days ago by
Jeremy Leipzig
22k • written 5 days ago by
Ali
• 0
3
votes
3
replies
257
views
getting exon coordinates
genomics
updated 5 days ago by
Ram
44k • written 5 days ago by
Xbox_27
• 0
0
votes
4
replies
341
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 4 days ago by
Tony
• 0 • written 5 days ago by
vk
▴ 10
1
vote
5
replies
333
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 4 days ago by
Ram
44k • written 5 days ago by
manuelmourato25
• 0
3
votes
4
replies
426
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR
masspec
uORF
peptide
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Pierre Lindenbaum
161k
180 results • Page
2 of 4
Recent Votes
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
Comment: Practical Haplotype Graph v2 not finding correct paths
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Recent Replies
Answer: z-score of gene set
by
Matthias Zepper
4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Pierre Lindenbaum
161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set
by
bk11
★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB
by
DBScan
▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results
by
Bjorn
• 0
Thank you!
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths
by
beantkapoor16
▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file
by
pirku
• 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice
by
GenoMax
142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file
by
Pierre Lindenbaum
161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line
by
Arthur
• 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long
by
Nitin Narwade
★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
▴ 220
The timing for your question is excellent. The fix was released yesterday.
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