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311 results • Page
5 of 7
Sort: Votes
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Votes
Replies
0
votes
3
replies
325
views
KEGG Pathways
r
RNA-seq
updated 18 days ago by
Ram
43k • written 19 days ago by
Sudip
• 0
0
votes
1
reply
162
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 5 days ago by
GenoMax
142k • written 5 days ago by
cedric.blais
• 0
0
votes
0
replies
154
views
Empty table plot using plotGseaTable()
FGSEA
15 days ago by
Chris
▴ 280
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
6 days ago by
atariw
▴ 10
0
votes
0
replies
190
views
CellPhoneDB results
cellphonedb
cpdb
cell_surface_proteins
updated 12 days ago by
GenoMax
142k • written 12 weeks ago by
piotto
▴ 20
0
votes
0
replies
163
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
16 days ago by
rustykb
▴ 20
0
votes
9
replies
606
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
3 days ago by
Arton
▴ 10
0
votes
0
replies
284
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 26 days ago by
Ram
43k • written 15 months ago by
Pine
▴ 20
0
votes
0
replies
145
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
9 days ago by
singcell
• 0
0
votes
0
replies
141
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 19 days ago by
Ram
43k • written 19 days ago by
Alexandros
• 0
0
votes
1
reply
274
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 12 days ago by
GenoMax
142k • written 12 days ago by
Sony
▴ 10
0
votes
0
replies
135
views
How to implement an IGV to streamlit app?
python
streamlit
igv
13 days ago by
avigail.shnaider
• 0
0
votes
3
replies
324
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 19 days ago by
GenoMax
142k • written 19 days ago by
kim
• 0
0
votes
1
reply
228
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 8 days ago by
curious
▴ 750 • written 9 days ago by
SeoGyun
• 0
0
votes
0
replies
90
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
1 day ago by
Moinuddin
• 0
0
votes
0
replies
140
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
3 days ago by
ebertomeup
• 0
0
votes
4
replies
426
views
Highest variable features in single cell data
single-cell
12 days ago by
carolofharvest
▴ 40
0
votes
0
replies
210
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 29 days ago by
Ram
43k • written 29 days ago by
mja
• 0
0
votes
3
replies
368
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 20 days ago by
Ram
43k • written 5 months ago by
Fadi
• 0
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
6 days ago by
gernophil
▴ 80
0
votes
2
replies
172
views
What marks a De-Novo Genome assembly as FAILED?
nanopore
denovo
illumina
assembly
genome
1 hour ago by
Umer
▴ 50
0
votes
6
replies
503
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 25 days ago by
gv
• 0 • written 6 weeks ago by
Srinka
▴ 20
0
votes
6
replies
320
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
0
votes
2
replies
283
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 8 days ago by
GenoMax
142k • written 15 days ago by
Ximena
• 0
0
votes
1
reply
157
views
input file for alternative splicing in rmats in linux
rmats
updated 10 days ago by
Ram
43k • written 10 days ago by
Lambodarswain316
• 0
0
votes
0
replies
114
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Rodolfo Adrián
• 0
0
votes
0
replies
119
views
vg call vs vg surject
vg
variation
graphs
updated 20 days ago by
GenoMax
142k • written 20 days ago by
aliraza3119
• 0
0
votes
0
replies
107
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
20 days ago by
Sara
▴ 30
0
votes
3
replies
210
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 12 days ago by
GenoMax
142k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
111
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
17 days ago by
Vijith
▴ 30
0
votes
0
replies
89
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
6 days ago by
JACKY
▴ 140
0
votes
0
replies
130
views
Help interpreting KEGG module definitions for converting to NetworkX graph
definition
kegg
module
database
genomics
2 days ago by
O.rka
▴ 720
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 20 days ago by
Ram
43k • written 9 months ago by
Gio
• 0
0
votes
0
replies
139
views
cat-bgen fail
bgenix
updated 3 days ago by
Ram
43k • written 3 days ago by
lambard
• 0
0
votes
0
replies
122
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
10 days ago by
asalimih
▴ 60
0
votes
0
replies
226
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
23 days ago by
HarperReed
• 0
0
votes
2
replies
312
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 16 days ago by
yahn
• 0
0
votes
1
reply
165
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 11 days ago by
Bastien Hervé
5.3k • written 11 days ago by
sooni
▴ 20
0
votes
0
replies
117
views
vdjtools
vdjtools
13 days ago by
yueli7
▴ 250
0
votes
0
replies
84
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 23 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
Mohamed Samir
▴ 20
0
votes
5
replies
433
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
25 days ago by
njornet
▴ 20
0
votes
1
reply
163
views
How to process Bulk WES data?
WES
WGS
updated 5 days ago by
GenoMax
142k • written 5 days ago by
wyuan37
• 0
0
votes
1
reply
80
views
Add stats to the plot
R
stats
plotting
updated 4 hours ago by
GenoMax
142k • written 7 hours ago by
Ghada
• 0
0
votes
0
replies
57
views
problems in installing rDock
rDock
make
Installation
Error
10 hours ago by
Rodolfo Adrián
• 0
0
votes
5
replies
286
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 11 days ago by
Joe
21k • written 11 days ago by
Lemonhope
• 0
0
votes
5
replies
327
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by
SilhouetteQ
• 0
0
votes
1
reply
207
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 8 days ago by
Ram
43k • written 8 days ago by
Shwetha
• 0
0
votes
1
reply
49
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
updated 20 minutes ago by
ATpoint
82k • written 5 hours ago by
Bibi
• 0
0
votes
0
replies
189
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
10 days ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
610
views
Differential accessibility using DiffBinf
diffbind
20 days ago by
Shloka
• 0
311 results • Page
5 of 7
Recent Votes
plotting trees in R: node labels from nexus tree files
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?
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Popular Question
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carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
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Muhammad
• 0
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synat.keam
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★ 1.8k
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Recent Replies
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
by
ATpoint
82k
I cannot give a precise answer, as ML is not my field, but generally, why don't you apply the method to pseudobulks of the exact single-cel…
Answer: geom_bar issue in ggplot2 with xlim()
by
ATpoint
82k
https://stackoverflow.com/questions/10365167/geom-bar-bars-not-displaying-when-specifying-ylim
Comment: What marks a De-Novo Genome assembly as FAILED?
by
Umer
▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
by
marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
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.
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