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1,155 results • Page
2 of 24
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Views
Votes
Replies
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 19 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 6 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 6 days ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 3 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 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 6 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab
benchmark
fastq
wgs
data-access
updated 20 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 27 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 25 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 27 days ago by
Ram
43k • written 9.4 years ago by
galbarel
▴ 10
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 13 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 4 days ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 13 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
2
votes
6
replies
5.2k
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 4 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
2
votes
3
replies
5.1k
views
BLAST Ring Image Generator (BRIG) error
error
software
alignment
updated 20 days ago by
GenoMax
141k • written 7.4 years ago by
casley_queiroz
▴ 20
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 12 days ago by
kaaz
• 0 • written 5.5 years ago by
ste.lu
▴ 80
1
vote
7
replies
5.0k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python
seaborn
updated 12 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 12 days ago by
jack
• 0 • written 7.5 years ago by
denalitastic
▴ 30
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 4 days 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 6 days ago by
Ram
43k • written 4.9 years ago by
WouterDeCoster
47k
4
votes
14
replies
4.8k
views
8 follow
Installation: Tax4Fun2 package are not found and github repository is not maintained anymore
Tax4Fun2
updated 26 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 6 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 6 days ago by
Ram
43k • written 6.6 years ago by
grant.hovhannisyan
★ 2.6k
7
votes
5
replies
4.6k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 50
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
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake
ngs
updated 7 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 5 days 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 28 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 6 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 13 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 13 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
14 days ago by
firestar
★ 1.6k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 13 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 13 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 4 days 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 27 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 4 days 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 4 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
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
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 13 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 6 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 5 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
1
vote
10
replies
3.9k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 9 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 7 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 6 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 4 days ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
1
vote
3
replies
3.7k
views
MSF Data Analysis
MSF
Proteomics
Thermo
Proteome Discoverer
updated 19 days ago by
iqra
• 0 • written 4.4 years ago by
JJDollar
▴ 130
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 13 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
2
votes
6
replies
3.6k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 6 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
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
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 4 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
1,155 results • Page
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Comment: Failed kmer content
Using vg gamsort with naive sorting algorithm
Answer: Using vg gamsort with naive sorting algorithm
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Interested in Spatial Omics?
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Answer: Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
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Comment: Subset Seurat object from Xenium spatial data
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For subsetting a sample, you can do something like this- Idents(seuratObj) <- "orig.ident" subj1 <- c("subject_1") subj1_seur…
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In modeller we need to use templates as well.so 63% is acceptable
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These regions are present in the genome and removing them might incorrectly redirect alignments to known genes. I don't see why you would r…
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Ok thank you! Do you know if there is an easy way of doing so with ncbi-genome-download or I need to use another tool?
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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: Redirection of Duplicate PMIDs
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
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anovak
▴ 120
The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file. To fin…
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I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
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Yes you can remove those if you are only interested in annotated genes.
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by
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[This could help][1] [1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
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