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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
110
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 10 days ago by
Ram
43k • written 10 days ago by
mathavanbioinfo
▴ 90
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 11 days ago by
chloek88
• 0 • written 5.6 years ago by
Philipp Bayer
8.5k
5
votes
7
replies
502
views
RNA seq analysis
DESeq
RNA-seq
4 days ago by
Jacek
▴ 20
0
votes
0
replies
147
views
Chance for trained without experience
bio
updated 11 days ago by
ATpoint
82k • written 11 days ago by
shehab
• 0
0
votes
0
replies
128
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
11 days ago by
Omics data mining
▴ 260
0
votes
2
replies
192
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
11 days ago by
njornet
▴ 20
0
votes
2
replies
219
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 10 days ago by
Adam
▴ 30 • written 11 days ago by
Darya
• 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
0
replies
182
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
10 days ago by
Winter
• 0
0
votes
0
replies
108
views
meffil.snp.concordance
meffil
methylation
snp_concordance
11 days ago by
kyj222637
• 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
1
vote
3
replies
265
views
STAR aligner error
RNA-seq
STAR
slurm
updated 10 days ago by
Ram
43k • written 11 days ago by
M.
▴ 30
0
votes
0
replies
103
views
monocle 3-- Could not get node in small cluster
monocle3
11 days ago by
synat.keam
▴ 100
0
votes
2
replies
225
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
11 days ago by
Nicholas
• 0
0
votes
1
reply
272
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
5
votes
5
replies
343
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
11 days ago by
Chris
▴ 280
0
votes
2
replies
241
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 10 days ago by
swbarnes2
14k • written 12 days ago by
ahmad.sajad4541
• 0
1
vote
9
replies
426
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 9 days ago by
i.sudbery
19k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
183
views
student
epitranscriptomics
updated 12 days ago by
ATpoint
82k • written 12 days ago by
useriwa
• 0
0
votes
3
replies
208
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
4
replies
314
views
Correlation Analysis
statistics
methylation
NGS
expression
8 days ago by
Researcher
▴ 30
1
vote
2
replies
205
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
12 days ago by
robert.flynn.21
• 0
0
votes
0
replies
130
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
12 days ago by
Scott McKay
▴ 30
0
votes
0
replies
116
views
Cellphonedb results
cpdb
visulization
cellphonedb
12 days ago by
piotto
▴ 20
0
votes
0
replies
128
views
Cox Model with interaction item interpretation
Cox
13 days ago by
Bine
▴ 60
0
votes
0
replies
115
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
10 days ago by
Javier
• 0
1
vote
7
replies
572
views
Question regarding WGCNA
WGCNA
Network-construction
10 days ago by
deepak
• 0
0
votes
0
replies
116
views
vdjtools
vdjtools
13 days ago by
yueli7
▴ 250
0
votes
1
reply
314
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 12 days ago by
andres.firrincieli
3.6k • written 13 days ago by
Antonio
• 0
0
votes
0
replies
130
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 13 days ago by
Ram
43k • written 13 days ago by
sidrah.maryam
▴ 50
0
votes
0
replies
112
views
Normalizing AMR gene count data
abundance
RGI
updated 13 days ago by
Ram
43k • written 13 days ago by
arshad1292
▴ 100
1
vote
1
reply
192
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
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
0
replies
140
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
13 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
130
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
14 days ago by
Christopher
• 0
0
votes
0
replies
132
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
14 days ago by
DGTool
▴ 20
2
votes
3
replies
354
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 9 days ago by
bk11
★ 2.5k • written 14 days ago by
Yoosef
▴ 60
0
votes
1
reply
286
views
creating batch colum for batch correction
batch-correction
combat
13 days ago by
Expert
▴ 10
0
votes
1
reply
249
views
Help with DGEList function
DGEList
R
updated 13 days ago by
marco.barr
▴ 130 • written 15 days ago by
Natali
• 0
0
votes
0
replies
173
views
Homer motif analysis
Homer
15 days ago by
daffodil
▴ 10
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
224
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 15 days ago by
Ram
43k • written 15 days ago by
Valentina
• 0
0
votes
6
replies
493
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 15 days ago by
swbarnes2
14k • written 16 days ago by
Erina
• 0
1
vote
3
replies
345
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
1
vote
0
replies
161
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 13 days ago by
zx8754
11k • written 15 days ago by
Emilie
▴ 10
0
votes
0
replies
150
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
16 days ago by
Javier
• 0
0
votes
2
replies
311
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
0
replies
142
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
16 days ago by
mikemakaveli1
• 0
2
votes
2
replies
254
views
Raw counts using stringtie
stringtie
RNA-seq
updated 16 days ago by
GenoMax
142k • written 16 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
141
views
Modify plot R mtDNA indel
plot
mtDNA
R
16 days ago by
marco.barr
▴ 130
1,000 results • Page
3 of 20
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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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.
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.…
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