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1,000 results • Page
4 of 20
Sort: Votes
Rank
Views
Votes
Replies
4
votes
2
replies
286
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 10 days ago by
Ram
43k • written 11 days ago by
Adi
▴ 10
4
votes
7
replies
593
views
UK biobank versus Genomics England
WGS
DRAGEN
GenomicsEngland
UK-BRAP
vcf
written 12 weeks ago by
zizigolu
★ 4.3k
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 11 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
4
votes
6
replies
448
views
Odd results with BLAST remote
blast
remote
NCBI
updated 11 days ago by
b.contreras.moreira
▴ 170 • written 12 days ago by
Begonia_pavonina
▴ 150
4
votes
4
replies
411
views
Problem generating paired end reads when converting Cell Ranger's BAM result to FASTQ
fastq
bam
28 days ago by
ntuzov
• 0
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 21 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 22 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
4
replies
465
views
Error Codes in Snakemake
python
snakemake
21 days ago by
888pea
▴ 10
4
votes
4
replies
365
views
Average expression of a sample in single-cell data
single-cell
rna-seq
24 days ago by
newuser2024
• 0
4
votes
4
replies
401
views
How do I install plink2 on a mac?
plink2
plink
updated 12 days ago by
zx8754
11k • written 14 days ago by
emilija.romic
▴ 10
4
votes
6
replies
837
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 24 days ago by
Ram
43k • written 5 months ago by
cee28
▴ 30
4
votes
4
replies
335
views
How to fetch published paper of a BioProject
BioProject
pumbed
NGS
17 days ago by
Morteza
• 0
4
votes
2
replies
372
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 1 day ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
4
votes
2
replies
322
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 9 days ago by
Juke34
8.5k • written 9 days ago by
njornet
▴ 20
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 8 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
4
votes
5
replies
359
views
merging tetraploid vcf files through bcftools
vcf
bcftools
25 days ago by
analyst
▴ 30
4
votes
13
replies
869
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 10 days ago by
BioinfGuru
★ 1.7k • written 16 days ago by
matteo.levorato
• 0
4
votes
4
replies
359
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 15 days ago by
colindaven
6.4k • written 24 days ago by
Md Moinuddin
• 0
4
votes
2
replies
1.2k
views
Tool:
Introducing Cramino: a *fast* QC tool for long reads
long-read
nanopore
pacbio
updated 21 days ago by
Ram
43k • written 18 months ago by
WouterDeCoster
47k
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
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 12 days ago by
GenoMax
141k • written 15 months ago by
Estefania
▴ 30
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic
Gene-Ontology
GO
updated 15 days ago by
Ram
43k • written 2.0 years ago by
ramin.k2013
• 0
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 10 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
3
votes
3
replies
779
views
GATK error on HPC clusters
variant-calling
SNP
updated 24 days ago by
Ram
43k • written 12 months ago by
princy149
• 0
3
votes
2
replies
584
views
News:
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
mathematical-modelling
endocrinology
ML
systems-biology
machine-learning
28 days ago by
Johannes W. Dietrich
• 0
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 8 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
4
replies
394
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness
contamination
22 days ago by
beacamara
• 0
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR
differential-gene-expression
edgeR
miRNA
updated 17 days ago by
Ram
43k • written 4.9 years ago by
AngAdd
▴ 20
3
votes
3
replies
719
views
KissDE and batch effect
kissDE
kissplice
5 days ago by
david.b.rombaut
▴ 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 10 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
3
votes
6
replies
8.4k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 10 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
3
votes
3
replies
318
views
How do I find up-to-date gene symbols for outdated names
names
symbols
gene
20 days ago by
DSmith
• 0
3
votes
4
replies
374
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 13 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
Sony
▴ 10
3
votes
5
replies
551
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
5 days ago by
n_navy
• 0
3
votes
4
replies
356
views
Single cell analysis with "meta".tsv.gz file
Single-cell
24 days ago by
Estevão
• 0
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 17 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 8 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
10
replies
614
views
Piping samtools to R
R
NGS
bash
samtools
10 days ago by
joe
▴ 510
3
votes
2
replies
335
views
kraken2 vs krakenuniq
KrakenUniq
kraken2
21 days ago by
pinheirofabiano
▴ 20
3
votes
7
replies
525
views
Artificial deletion in bam
bam
updated 21 days ago by
Zhenyu Zhang
★ 1.2k • written 22 days ago by
enee
▴ 10
3
votes
2
replies
275
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
5 days ago by
kristiewyleung
• 0
3
votes
1
reply
871
views
Fisher exact test in R package
Fisher-test
updated 24 days ago by
Ram
43k • written 2.9 years ago by
Nuglozeh
▴ 10
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 10 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
5
replies
475
views
Having trouble building VG in Ubuntu
vg
updated 13 days ago by
Ram
43k • written 16 days ago by
ayushm64
• 0
3
votes
3
replies
471
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 7 days ago by
swbarnes2
14k • written 8 days ago by
joe
▴ 510
3
votes
3
replies
188
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 1 day ago by
GenoMax
141k • written 1 day ago by
sapuizait
▴ 10
3
votes
3
replies
337
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
15 days ago by
george
• 0
3
votes
2
replies
812
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 10 days ago by
Ram
43k • written 3.2 years ago by
helia.ziaei
• 0
1,000 results • Page
4 of 20
Recent Votes
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Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
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★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
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▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
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• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
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by
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They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
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https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
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Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
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Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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