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371 results • Page
4 of 8
Sort: replies
Rank
Views
Votes
Replies
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 2 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
2
votes
3
replies
347
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 4 days ago by
ATpoint
81k • written 5 days ago by
IM
• 0
1
vote
3
replies
267
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 2 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
giulia.cosenza
• 0
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST
E-value
Blastp
Protein
updated 2 days ago by
Ram
43k • written 5.3 years ago by
minasmayth
• 0
2
votes
3
replies
253
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 2 days ago by
Michael
54k • written 2 days ago by
LDT
▴ 330
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat
CNA
Batch-Effect
updated 1 day ago by
Ram
43k • written 5.5 years ago by
sugus
▴ 150
2
votes
3
replies
370
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
1 day ago by
valentinatsar
• 0
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 4 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 4 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 23 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 23 hours ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
0
votes
2
replies
262
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
3
votes
2
replies
224
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
3 hours ago by
joe
▴ 510
0
votes
2
replies
1.2k
views
Normalization (microarray data)
microarray
Normalization
Batch-effect
updated 23 hours ago by
Ram
43k • written 6.3 years ago by
j_jamal96
▴ 20
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 23 hours ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
1
vote
2
replies
165
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
2 days ago by
hagl
▴ 10
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq
edgeR
R
Batch-Effect
updated 1 day ago by
Ram
43k • written 5.6 years ago by
sckinta
▴ 730
0
votes
2
replies
204
views
Getting marker genes for cell types
clustering
marker-genes
umap
3 days ago by
orzrzlyo
▴ 20
0
votes
2
replies
257
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
6 days ago by
ramin.k2013
• 0
4
votes
2
replies
3.7k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 23 hours ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
0
votes
2
replies
268
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 7 days ago by
Apollonia
• 0
0
votes
2
replies
213
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
2 days ago by
mropri
▴ 150
0
votes
2
replies
262
views
Adding CB tag to bam file
samtools
bam
8 hours ago by
Maria
• 0
1
vote
2
replies
311
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 9 hours ago by
Pierre Lindenbaum
161k • written 20 hours ago by
rahu
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 2 days ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
0
votes
2
replies
266
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
11 hours ago by
Ashok
• 0
0
votes
2
replies
322
views
How can I solve this error?
metal
1 day ago by
22211020193
• 0
0
votes
2
replies
248
views
python file for coding potential calculator
cpc2.py
13 hours ago by
Ashok
• 0
0
votes
2
replies
213
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
2 days ago by
DKA
▴ 40
0
votes
2
replies
242
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
13 hours ago by
Ashok
• 0
0
votes
2
replies
386
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
17 hours ago by
航太郎
• 0
0
votes
2
replies
184
views
Bedmethyl file format
bedmethyl
methylation
updated 2 days ago by
GenoMax
141k • written 2 days ago by
njornet
▴ 20
0
votes
2
replies
286
views
GSEA analysis in R
GSEA
R
Arabidopsis
1 day ago by
Sudip
• 0
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 2 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
0
votes
2
replies
517
views
autodockvina
python
python3
autodock
updated 21 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
4
votes
2
replies
276
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 1 day ago by
Juke34
8.5k • written 1 day ago by
njornet
▴ 20
0
votes
2
replies
316
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 1 day ago by
Ehsan
• 0 • written 8 weeks ago by
bioinfo
▴ 150
1
vote
2
replies
322
views
Forum:
VCF bulk handling
bcftools
SnpEff
WGS
VEP
VCF
2 days ago by
Javier
• 0
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 2 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 23 hours ago by
Ram
43k • written 9.1 years ago by
chengzhao41
▴ 110
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva
svaseq
batch-effect
updated 23 hours ago by
Ram
43k • written 6.8 years ago by
wamiqsaifi
• 0
2
votes
2
replies
193
views
Problem with Sniffles pipeline and SV calling help
SV
sniffles
StructuralVariant
updated 4 days ago by
GenoMax
141k • written 4 days ago by
njornet
▴ 20
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 2 days ago by
Ram
43k • written 3.7 years ago by
svp
▴ 680
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 23 hours ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 23 hours ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
2
votes
2
replies
245
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
3 days ago by
bioinfo
▴ 150
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 23 hours ago by
Ram
43k • written 3.7 years ago by
i.sudbery
19k
1
vote
2
replies
1.8k
views
Data processing order: normalisation or batch effect correction first?
limma
proteome
batch-effect
R
updated 2 days ago by
Ram
43k • written 3.5 years ago by
Sebastian Hesse
▴ 340
0
votes
2
replies
343
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
2 days ago by
arriyaz.nstu
▴ 30
371 results • Page
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Recent Votes
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
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Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Done. Thank you.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
GenoMax
141k
Perhaps add the word linux/ubuntu to the title? You have noted that the instructions are for Ubuntu in text.
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
BioinfGuru
★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
Comment: Downloading the raw microarray data from GEO
by
GenoMax
141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
GenoMax
141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
by
bp22
▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
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Ram
43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately?
by
Ram
43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis
by
BioinfGuru
★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
by
Mohamed Abderrahmane
▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
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Enrique
• 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
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ATpoint
81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
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by
joe
▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort
by
ATpoint
81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
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