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1,000 results • Page
4 of 20
Sort: Votes
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Views
Votes
Replies
4
votes
0
replies
867
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
14 days ago by
Wubin
▴ 40
4
votes
14
replies
4.8k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 28 days ago by
Ram
43k • written 22 months ago by
Elsa
▴ 20
4
votes
7
replies
543
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 20 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
4
replies
354
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 13 days ago by
colindaven
6.4k • written 22 days ago by
Md Moinuddin
• 0
4
votes
4
replies
463
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 13 days ago by
damian.szk
▴ 70 • written 13 days ago by
rohitsatyam102
▴ 840
4
votes
2
replies
1.2k
views
Tool:
Introducing Cramino: a *fast* QC tool for long reads
long-read
nanopore
pacbio
updated 19 days ago by
Ram
43k • written 17 months ago by
WouterDeCoster
47k
4
votes
6
replies
443
views
Odd results with BLAST remote
blast
remote
NCBI
updated 9 days ago by
b.contreras.moreira
▴ 170 • written 10 days ago by
Begonia_pavonina
▴ 150
4
votes
5
replies
349
views
merging tetraploid vcf files through bcftools
vcf
bcftools
23 days ago by
analyst
▴ 30
4
votes
2
replies
316
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 7 days ago by
Juke34
8.5k • written 7 days ago by
njornet
▴ 20
4
votes
3
replies
7.4k
views
How to find/decipher Trimmomatic Output
trimmomatic
RNA-Seq
QC
updated 26 days ago by
Ram
43k • written 8.1 years ago by
nikelle.petrillo
▴ 110
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 15 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
4
votes
4
replies
358
views
Average expression of a sample in single-cell data
single-cell
rna-seq
22 days ago by
newuser2024
• 0
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 10 days ago by
GenoMax
141k • written 15 months ago by
Estefania
▴ 30
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 8 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 16 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
4
replies
461
views
Error Codes in Snakemake
python
snakemake
19 days ago by
888pea
▴ 10
4
votes
9
replies
1.1k
views
Error in openning FastQC
fastqc
igv
updated 27 days ago by
GenoMax
141k • written 8 months ago by
huynhthienphai
• 0
4
votes
11
replies
1.3k
views
Paired layout, but one fastq file
fastq
updated 28 days ago by
GenoMax
141k • written 13 months ago by
Andy
▴ 120
4
votes
4
replies
391
views
How do I install plink2 on a mac?
plink2
plink
updated 10 days ago by
zx8754
11k • written 12 days ago by
emilija.romic
▴ 10
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 19 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
4
votes
2
replies
225
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa
samtools
mapping
genome
updated 20 days ago by
Pierre Lindenbaum
161k • written 20 days ago by
Lee
• 0
3
votes
6
replies
891
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
3
votes
4
replies
649
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
2 days ago by
rahu
• 0
3
votes
9
replies
394
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
3
votes
1
reply
162
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 23 days ago by
GenoMax
141k • written 23 days ago by
dthorbur
★ 1.9k
3
votes
2
replies
811
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 8 days ago by
Ram
43k • written 3.2 years ago by
helia.ziaei
• 0
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 15 days ago by
Ram
43k • written 7.9 years ago by
1234anjalianjali1234
▴ 50
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
1
reply
596
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 7 days ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
3
votes
0
replies
109
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
3
votes
5
replies
463
views
Having trouble building VG in Ubuntu
vg
updated 11 days ago by
Ram
43k • written 14 days ago by
ayushm64
• 0
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 8 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
3
votes
7
replies
453
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
8 days ago by
ntsopoul
▴ 60
3
votes
3
replies
179
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
c_u
▴ 520
3
votes
3
replies
333
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
13 days ago by
george
• 0
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated just now by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 8 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 8 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
3
votes
5
replies
538
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
3 days ago by
n_navy
• 0
3
votes
3
replies
775
views
GATK error on HPC clusters
variant-calling
SNP
updated 22 days ago by
Ram
43k • written 12 months ago by
princy149
• 0
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq
batch-effect
DESeq2
updated 16 days ago by
Ram
43k • written 3.9 years ago by
annamariabugaj
• 0
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 19 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 910
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 8 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
3
votes
4
replies
352
views
Single cell analysis with "meta".tsv.gz file
Single-cell
22 days ago by
Estevão
• 0
3
votes
5
replies
408
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
updated 22 days ago by
GenoMax
141k • written 22 days ago by
e.r.zakiev
▴ 200
3
votes
3
replies
500
views
Korean human genome reference file
GWAS
reference
imputation
6 days ago by
SeoGyun
• 0
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
13
replies
638
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 22 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 6 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
1,000 results • Page
4 of 20
Recent Votes
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
Answer: What Is A "Spot" In Sra Format
Comment: Why gatk VariantAnnotator required bam and coverage files
Comment: Why gatk VariantAnnotator required bam and coverage files
discoSnp - reference-free finding of isolated SNPs from non assembled reads
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Comment: ScRNA data question
by
bk11
★ 2.3k
Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis?
by
sp
• 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
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