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1,000 results • Page
2 of 20
Sort: Views
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Views
Votes
Replies
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 22 hours ago by
Ram
43k • written 4.5 years ago by
Bogdan
★ 1.4k
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 22 hours ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 15 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 2 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 2 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 2 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
2
votes
7
replies
5.6k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab
benchmark
fastq
wgs
data-access
updated 16 days ago by
geocarvalho
▴ 360 • written 5.1 years ago by
Fungsten
• 0
6
votes
12
replies
5.6k
views
6 follow
Getting sample information from GEO
GEO
NCBI
updated 23 days ago by
Tania
• 0 • written 6.9 years ago by
Tom_L
▴ 350
9
votes
8
replies
5.6k
views
7 follow
CONTRA for CNV detection. troubleshooting
genome
next-gen-sequencing
cnv
software-error
updated 22 days ago by
Ram
43k • written 9.9 years ago by
Kizuna
▴ 870
5
votes
5
replies
5.5k
views
beagle 4 exception: Duplicate marker
vcf
IBD
plink
beagle
updated 23 days ago by
Ram
43k • written 9.4 years ago by
galbarel
▴ 10
8
votes
16
replies
5.3k
views
9 follow
visualize CNV data based on WGS
CNV
updated 29 days ago by
clealk
▴ 50 • written 6.3 years ago by
Bogdan
★ 1.4k
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 9 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 10 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
2
votes
3
replies
5.1k
views
BLAST Ring Image Generator (BRIG) error
error
software
alignment
updated 16 days ago by
GenoMax
141k • written 7.3 years ago by
casley_queiroz
▴ 20
2
votes
6
replies
5.1k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 22 hours ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
11
votes
8
replies
5.1k
views
Multi-mapping High with featureCounts but not STAR
RNA-Seq
sequencing
alignment
updated 29 days ago by
GenoMax
141k • written 4.9 years ago by
garbuzov
▴ 70
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 8 days ago by
kaaz
• 0 • written 5.5 years ago by
ste.lu
▴ 80
2
votes
7
replies
5.1k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 3 hours ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
1
vote
7
replies
5.0k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python
seaborn
updated 8 days ago by
Wubin
▴ 40 • written 3.4 years ago by
roy.granit
▴ 880
0
votes
1
reply
5.0k
views
How to compute a one tail (one way) log rank test for survival?
R
survival
hypothesis-testing
log-rank
updated 8 days ago by
jack
• 0 • written 7.5 years ago by
denalitastic
▴ 30
5
votes
15
replies
4.9k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq
IGV
mapping
updated 28 days ago by
vague-barracuda-4686
• 0 • written 4.8 years ago by
Apprentice
▴ 160
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 22 hours ago by
Ram
43k • written 9.6 years ago by
mjarosz
• 0
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 3 days ago by
Ram
43k • written 4.9 years ago by
WouterDeCoster
47k
4
votes
14
replies
4.7k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 22 days ago by
Ram
43k • written 22 months ago by
Elsa
▴ 20
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 2 days ago by
Ram
43k • written 5.8 years ago by
fp89
▴ 30
1
vote
2
replies
4.6k
views
predict TF binding sites from DNA sequence
TF
TRANSFAC
TFBS
binding-site
updated 2 days ago by
Ram
43k • written 6.6 years ago by
grant.hovhannisyan
★ 2.6k
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
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake
ngs
updated 3 days ago by
进
• 0 • written 3.9 years ago by
Peter Chung
▴ 200
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 5.9 years ago by
Poorya Parvizi
▴ 60
2
votes
2
replies
4.4k
views
Variant calling for sanger reads
variant-calling
sanger
alignment
variants
updated 24 days ago by
Ram
43k • written 7.7 years ago by
Amirosein
▴ 70
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
18
votes
20
replies
4.4k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray
differential-gene-expression
updated 10 days ago by
Ram
43k • written 7.5 years ago by
morteza.mahmoudisaber
▴ 80
12
votes
13
replies
4.4k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression
RNA-Seq
glm
DESeq2
updated 10 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics
10x
10 days ago by
firestar
★ 1.6k
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 10 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 10 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 23 hours ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 23 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 22 hours ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 22 hours ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 10 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 1 day ago by
Ram
43k • written 4.9 years ago by
Mozart
▴ 330
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 2 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
Rimma
▴ 30
1
vote
10
replies
3.8k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 5 days ago by
Aspire
▴ 300 • written 18 months ago by
Manav
• 0
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 3 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
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 2 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
7
votes
5
replies
3.8k
views
ISCN annotation for SV/CN VCF files
SV
updated 1 day ago by
adedare
• 0 • written 7 months ago by
a.beggs
▴ 50
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
2
votes
4
replies
3.7k
views
Tutorial for analysing gpr files of microarray
GPR
microarray
updated 28 days ago by
bioyas
▴ 10 • written 5.5 years ago by
afli
▴ 190
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Comment: Cellranger count error: Input FASTQ file ended prematurely
by
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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…
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Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
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Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
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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/
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▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
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by
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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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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joe
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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…
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by
ATpoint
81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
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by
Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort
by
tamas.malkocs
• 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
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by
Dinmukhamed
• 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
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