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525 results • Page
3 of 11
Sort: Votes
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Views
Votes
Replies
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT
Long-read-sequencing
NanoPlot
updated 14 days ago by
Ram
43k • written 2.2 years ago by
matt81rd
▴ 10
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva
microarrays
batch-effect
updated 2 days ago by
Ram
43k • written 6.8 years ago by
ATCG
▴ 380
1
vote
2
replies
249
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 23 days ago by
bioruffo
▴ 40 • written 25 days ago by
MAPK2
▴ 40
1
vote
2
replies
239
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 2 days ago by
Ram
43k • written 2 days ago by
aniigodwinn
• 0
1
vote
6
replies
496
views
Quest about the input data for PCA analysis
PCA
27 days ago by
tujuchuanli
▴ 100
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 17 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
1
vote
1
reply
158
views
permutation test in edgeR
rna-seq
edgeR
updated 11 days ago by
dariober
14k • written 11 days ago by
Netanel
• 0
1
vote
0
replies
177
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
21 days ago by
Shicheng Guo
★ 9.4k
1
vote
1
reply
407
views
Long reads Annotation
long-reads
pacbio
updated 14 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
1
vote
1
reply
185
views
Tool for gene function identification
Gene-Function
updated 17 days ago by
Ram
43k • written 17 days ago by
Estevão
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 1 day ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
1
vote
1
reply
186
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
4 days ago by
CTLong
▴ 110
1
vote
0
replies
148
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 8 days ago by
Ram
43k • written 8 days ago by
ian.will
▴ 30
1
vote
1
reply
468
views
Manta: What does all this mean
manta
Variant-calling
VEP
updated 17 days ago by
Ram
43k • written 8 months ago by
josh.mannheimer
• 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
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 2 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
1
vote
1
reply
310
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 29 days ago by
dthorbur
★ 1.9k • written 29 days ago by
ekirsch
• 0
1
vote
1
reply
593
views
accessing the global gut microbial gene catalogue (MEDUSA)
medusa
gene-catalogue
gut-microbiome
updated 8 days ago by
Ram
43k • written 3.2 years ago by
ramin.k2013
• 0
1
vote
0
replies
129
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 4 days ago by
Ram
43k • written 4 days ago by
Oscar
▴ 10
1
vote
2
replies
201
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 22 days ago by
Ram
43k • written 22 days ago by
gdfsnkfns
• 0
1
vote
0
replies
1.0k
views
interpretation of trajectory and batch effect
monocle3
batch-effect
trajectory
updated 11 days ago by
Ram
43k • written 3.5 years ago by
tushard1987
▴ 10
1
vote
0
replies
365
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 10 days ago by
Ram
43k • written 2.3 years ago by
michael.s
▴ 10
1
vote
2
replies
266
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 24 days ago by
bioruffo
▴ 40 • written 24 days ago by
Bunit
• 0
1
vote
1
reply
165
views
Failed to download data from EBI with ascp
EBI
aspera
updated 8 days ago by
GenoMax
141k • written 8 days ago by
biock
▴ 60
1
vote
1
reply
289
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
2 hours ago by
renan.igor
• 0
1
vote
2
replies
318
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 16 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
geocarvalho
▴ 360
1
vote
2
replies
819
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 17 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 6 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
Morteza
• 0
1
vote
3
replies
315
views
Ensembl gene id conversion
biomart
ensembl
updated 3 days ago by
ATpoint
81k • written 5 days ago by
naveedhasan2000
• 0
1
vote
2
replies
194
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
11 days ago by
phhelou5
• 0
1
vote
4
replies
270
views
Removing batch effect using combat-seq
batch
effect
RNA-Seq
combat-seq
updated 17 days ago by
BioinfGuru
★ 1.7k • written 18 days ago by
Netanel
• 0
1
vote
2
replies
1.2k
views
Multi-fasta file for gffread
gffread
gtf
fasta
updated 29 days ago by
alnam
▴ 10 • written 2.4 years ago by
Vitor1
▴ 120
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 4 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
1
vote
1
reply
156
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 3 days ago by
dsull
★ 5.8k • written 3 days ago by
niruf
• 0
1
vote
2
replies
910
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 14 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
7
replies
881
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 24 days ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
3
replies
257
views
True variants selection
vcf
bcftools
updated 7 days ago by
dthorbur
★ 1.9k • written 8 days ago by
maevalefeuvre
• 0
1
vote
1
reply
652
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 2 days ago by
Ram
43k • written 4.4 years ago by
s.lima.diogenes
▴ 10
1
vote
0
replies
111
views
Downloading immne signature and pathway signature genes form publication and KEGG
genes
TRANSCRIPTOME_signature
25 days ago by
mrazib0210
▴ 10
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 2 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
2
replies
261
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
3 days ago by
bp22
▴ 70
1
vote
1
reply
811
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 14 days ago by
Ram
43k • written 11 months ago by
shinyjj
▴ 50
1
vote
4
replies
344
views
Molecular docking with Autodock
Docking
proteomics
updated 14 days ago by
Ram
43k • written 11 weeks ago by
shwetamgr1
▴ 10
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 2 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
1
vote
0
replies
147
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
8 days ago by
eesiribloom
▴ 80
1
vote
0
replies
665
views
Conditions for valid batch effect correction
r
batch-effect
updated 2 days ago by
Ram
43k • written 5.1 years ago by
Sebastian Hesse
▴ 340
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 2 days ago by
Ram
43k • written 7.1 years ago by
mrodrigues.fernanda
▴ 50
1
vote
1
reply
204
views
Retrieve a % coverage for each transcript
RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
jammydodger123456
▴ 40
1
vote
3
replies
245
views
CCA with random effects model
CCA
updated 17 days ago by
dariober
14k • written 17 days ago by
leranwangcs
▴ 120
0
votes
0
replies
187
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 7 days ago by
Ram
43k • written 7 days ago by
roussine
▴ 10
525 results • Page
3 of 11
Recent Votes
Answer: Duplicate marking, read names, and the SRA
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?
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Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
> fastq-dump is deprecated Curios if there a reference for this? `fasterq-dump` seems to allow for parallel streams but `fastq-dump` is st…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
by
GenoMax
141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
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
by
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
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