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1,000 results • Page
2 of 20
Sort: Votes
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Views
Votes
Replies
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 4 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
9
votes
4
replies
264
views
Ubuntu storage space is decreasing automatically
ubuntu
storage
updated 13 days ago by
colindaven
6.4k • written 13 days ago by
analyst
▴ 20
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 5 days ago by
Ram
43k • written 4.9 years ago by
Mozart
▴ 330
9
votes
6
replies
1.5k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr
amplicon
primer
updated 20 days ago by
Ram
43k • written 16 months ago by
O.rka
▴ 710
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 6 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA
batch-effect
gene-expression
updated 14 days ago by
Ram
43k • written 3.5 years ago by
Gene_MMP8
▴ 240
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
5 days ago by
Ram
43k
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression
RNA-seq
updated 13 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
2
replies
761
views
News:
FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
17 days ago by
David Langenberger
11k
8
votes
3
replies
355
views
How to extract rows with specific values in R for all the columns?
R
19 days ago by
Lakshmi
▴ 20
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 5 days ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
8
votes
12
replies
3.5k
views
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
ATAC-seq
updated 20 days ago by
Maksim
• 0 • written 3.4 years ago by
progistar
▴ 40
8
votes
10
replies
682
views
bash script
whole-genome-sequencing
updated 7 days ago by
Ram
43k • written 14 days ago by
bestone
▴ 30
8
votes
6
replies
608
views
The bioinformatics paper reappears, but the results are significantly different from the original results
reproducibility
18 days ago by
jiao
▴ 40
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 7 days ago by
e.r.zakiev
▴ 200 • written 15 months ago by
liorglic
★ 1.4k
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 6 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
7
votes
4
replies
1.9k
views
AlphaFold 2 alternatives
protein-structure
alphafold
updated 20 days ago by
Ram
43k • written 17 months ago by
Dunois
★ 2.5k
7
votes
2
replies
250
views
Create a new reference genome with denovo assembly and standard reference with long read data?
PacBio
updated 27 days ago by
gconcepcion
▴ 410 • written 27 days ago by
eorr
▴ 30
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 6 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 5 days ago by
Ram
43k • written 4.8 years ago by
mosesoo
▴ 30
7
votes
8
replies
653
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
18 days ago by
Riq
▴ 50
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 11 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
7
votes
6
replies
409
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
1 day ago by
analyst
▴ 20
7
votes
7
replies
995
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 7 days ago by
Dunois
★ 2.5k • written 8 days ago by
AdviceSeeker
• 0
7
votes
8
replies
642
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 10 days ago by
spen
▴ 40 • written 13 days ago by
MBarcelo
▴ 40
7
votes
10
replies
2.6k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 6 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA
RNA-Seq
batch-effect
updated 5 days ago by
Ram
43k • written 5.1 years ago by
tujuchuanli
▴ 100
7
votes
3
replies
2.8k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 4 days ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 6 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 6 days ago by
Ram
43k • written 6.1 years ago by
mannoulag1
▴ 120
7
votes
7
replies
530
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 10 days ago by
Matthias Zepper
4.5k • written 10 days ago by
4fzcgueyp5
• 0
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt
getBM
R
updated 6 days ago by
Ram
43k • written 5.2 years ago by
Corentin
▴ 600
7
votes
5
replies
4.5k
views
ISCN annotation for SV/CN VCF files
SV
updated 5 days ago by
adedare
• 0 • written 7 months ago by
a.beggs
▴ 50
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 6 days ago by
Ram
43k • written 5.2 years ago by
Davide Chicco
▴ 120
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 5 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
6
votes
13
replies
587
views
Variant calling of GBS data
GBS
variants
BQSR
25 days ago by
analyst
▴ 20
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 17 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq
quantification
alignment
updated 6 days ago by
Ram
43k • written 5.1 years ago by
mohammedtoufiq91
▴ 250
6
votes
3
replies
150
views
Interpretting IGV output
IGV
updated 1 day ago by
Carlo Yague
8.7k • written 1 day ago by
analyst
▴ 20
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics
10x
13 days ago by
firestar
★ 1.6k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 6 days ago by
Ram
43k • written 9.5 years ago by
james.lloyd
▴ 100
6
votes
0
replies
2.6k
views
Tool:
Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression
batch-effect
immunology
updated 4 days ago by
Ram
43k • written 7.0 years ago by
alexis.vandenbon
▴ 80
6
votes
8
replies
521
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 5 days ago by
dariober
14k • written 8 days ago by
manaswiniparija3
▴ 40
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 6 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 4 days ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 14 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
6
votes
9
replies
1.8k
views
How to convert .wib files to .wig or .bed?
wib
BED
wig
bedtools
26 days ago by
Zeng Jingyu
▴ 60
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 5 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 13 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
6
votes
12
replies
5.6k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 27 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
1,000 results • Page
2 of 20
Recent Votes
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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No, in haplotypecaller
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Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
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> What is your suggestion to run GenomicsDBImport efficiently? call the GVCF by slices eg: chr1:1000000-2000000<br> run GenomicsDBImport …
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The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
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Show us the exact call to `cnetplot()` with a sample of all input parameters. Did you compare notes with your friend?
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