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193 results • Page
3 of 4
Sort: replies
Rank
Views
Votes
Replies
1
vote
2
replies
1.6k
views
Seurat CellCycleScoring – confused about the proper order of operations when using SCTransform
CellCycleScoring
SCTransform
Seurat
updated 1 day ago by
Li
• 0 • written 2.3 years ago by
GPM
▴ 10
0
votes
2
replies
223
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Prawesh
• 0
0
votes
2
replies
166
views
Server or aws cloud- which one is better for gatk pipeline
aws
server
calling
gatk
cloud
updated 1 day ago by
Michael
54k • written 1 day ago by
ashaneev07
▴ 20
0
votes
2
replies
132
views
Presence of unknown sites in ANNOVAR output file
ANNOVAR
updated 20 hours ago by
GenoMax
142k • written 21 hours ago by
sainavyav22
• 0
5
votes
2
replies
97
views
EdgeR - relationship between logFC and coefficients
differential-expression
r
edger
updated 8 hours ago by
Gordon Smyth
★ 7.1k • written 10 hours ago by
gBioStar5
▴ 10
0
votes
2
replies
90
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
6 hours ago by
jain72744
▴ 10
0
votes
1
reply
72
views
Microbial Signal Transduction Database
MiST
updated 4 hours ago by
zx8754
11k • written 6 hours ago by
Shravani
• 0
0
votes
1
reply
275
views
Snakemake fails to find conda in PBS
snakemake
updated 20 hours ago by
tim.booth
▴ 60 • written 28 days ago by
yixinzeng
• 0
0
votes
1
reply
152
views
Enhanced Volcano-Cut off
foldchange
enhancedvolcano
updated 1 day ago by
marco.barr
▴ 100 • written 1 day ago by
odi
▴ 10
0
votes
1
reply
261
views
creating batch colum for batch correction
batch-correction
combat
4 days ago by
Expert
▴ 10
0
votes
1
reply
139
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
updated 1 day ago by
Bastien Hervé
5.3k • written 2 days ago by
sooni
▴ 20
1
vote
1
reply
251
views
Seurat V5 integration
Seurat
integration
updated 1 day ago by
Ram
43k • written 5 days ago by
starswillfade
▴ 10
2
votes
1
reply
307
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 6 days ago by
chrchang523
10k • written 10 days ago by
8armed
▴ 10
1
vote
1
reply
191
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 5 days ago by
Ram
43k • written 7 days ago by
adi.gershon1
• 0
0
votes
1
reply
130
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 3 days ago by
LChart
3.9k • written 3 days ago by
David
• 0
0
votes
1
reply
215
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 5 days ago by
Ram
43k • written 6 days ago by
Rob
▴ 170
1
vote
1
reply
203
views
Gene ontology and homologs
gene-ontology
updated 3 days ago by
geneontologyhelp
▴ 400 • written 4 days ago by
beshka194
• 0
1
vote
1
reply
401
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 1 day ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
0
votes
1
reply
237
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Thanujay S
• 0 • written 6 days ago by
yahn
• 0
0
votes
1
reply
202
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 6 days ago by
Ram
43k • written 6 days ago by
Valentina
• 0
4
votes
1
reply
240
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 4 days ago by
zx8754
11k • written 5 days ago by
Jautis
▴ 560
1
vote
1
reply
208
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 3 days ago by
Michael
54k • written 3 days ago by
Guillermo
• 0
0
votes
1
reply
206
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 6 days ago by
GenoMax
142k • written 6 days ago by
Ximena
• 0
1
vote
1
reply
157
views
student
epitranscriptomics
updated 3 days ago by
ATpoint
82k • written 3 days ago by
useriwa
• 0
0
votes
1
reply
213
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Sony
▴ 10
0
votes
1
reply
301
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 4 days ago by
aaron.stevens
• 0 • written 3 months ago by
sativus
▴ 20
0
votes
1
reply
80
views
DESeq2 error
DESeq2
updated 7 hours ago by
ATpoint
82k • written 10 hours ago by
sooni
▴ 20
0
votes
1
reply
282
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 3 days ago by
andres.firrincieli
3.6k • written 4 days ago by
Antonio
• 0
0
votes
1
reply
225
views
Help with DGEList function
DGEList
R
updated 4 days ago by
marco.barr
▴ 100 • written 6 days ago by
Natali
• 0
0
votes
1
reply
164
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
MAPK2
▴ 40
0
votes
1
reply
21
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 1 hour ago by
GenoMax
142k • written 1 hour ago by
maria.soler
• 0
0
votes
1
reply
243
views
barcode of TCR-sequencing
barcode
updated 2 days ago by
mizraelson
▴ 60 • written 10 days ago by
yueli7
▴ 250
0
votes
1
reply
161
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 1 day ago by
marco.barr
▴ 100 • written 1 day ago by
elisheva
▴ 120
0
votes
1
reply
544
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 5 days ago by
GenoMax
142k • written 5 days ago by
tulip
• 0
0
votes
1
reply
92
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 5 hours ago by
ATpoint
82k • written 8 hours ago by
Amr
▴ 160
7
votes
1
reply
154
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 3 days ago by
dariober
14k • written 3 days ago by
nhaus
▴ 360
3
votes
1
reply
60
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 1 hour ago by
dthorbur
★ 1.9k • written 13 hours ago by
Eren
• 0
1
vote
1
reply
118
views
Conda severely broken after attempting mamba install
biopython
conda
mamba
pycosat
updated 1 day ago by
andres.firrincieli
3.6k • written 1 day ago by
kacollier
▴ 30
0
votes
1
reply
95
views
input file for alternative splicing in rmats in linux
rmats
updated 21 hours ago by
Ram
43k • written 1 day ago by
Lambodarswain316
• 0
2
votes
1
reply
125
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
2 days ago by
analyst
▴ 50
0
votes
0
replies
140
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
6 days ago by
Javier
• 0
0
votes
0
replies
121
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
5 days ago by
DGTool
• 0
2
votes
0
replies
59
views
News:
course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics
SNPs
LocalAdaptation
GIS
18 hours ago by
carlopecoraro2
★ 2.5k
3
votes
0
replies
1.1k
views
Tool:
Sars-Cov-2 Genome & ACE 2 Exploration
sequence
alignment
SNP
genome
5 days ago by
Ibrahim Tanyalcin
★ 1.2k
0
votes
0
replies
62
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization
Mendelian
two-sample
18 hours ago by
Nikki
• 0
0
votes
0
replies
58
views
supervised admixture
supervised
admixture
16 hours ago by
RT
▴ 10
0
votes
0
replies
52
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
14 hours ago by
Aytaç
• 0
0
votes
0
replies
156
views
Homer motif analysis
Homer
6 days ago by
daffodil
▴ 10
0
votes
0
replies
37
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
8 hours ago by
jain72744
▴ 10
0
votes
0
replies
37
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
8 hours ago by
singcell
• 0
193 results • Page
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Recent Votes
Comment: Question about methylation location
Comment: Question about methylation location
How to use minimap2?
Comment: RNA seq analysis
Comment: Filtering Multi-sample VCF file for all except one Genotype
Truncated metadata file report from ENA Portal API
Comment: Truncated metadata file report from ENA Portal API
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Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
With the `--read2-only` option (which isn't available yet on the bioconda version), this will complain about a lack of `--bc-pattern`. How…
Comment: samtools tview symbols
by
Ruqaiya
• 0
What does the star mean then ?
Comment: RNA seq analysis
by
prifa
▴ 10
it's raw data **fastq.gz**, so for example I have 4 different samples from different tissue, sample A with 3 replicates, samples B,C and D …
Answer: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> The goal is to remove all the variants which are unique to the KWSBambina sample. using jvarkit vcffilterjdk https://jvarkit.readthedo…
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
The first example used the adapter file NexteraPE-PE.fa, but it generated more than 50% unpaired data...... The content of NexteraPE-PE.fa…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Ok so I definitely didn't understand at first what my goal was. The goal is to remove all the variants which are unique to the KWSBambina…
Comment: Question about methylation location
by
dthorbur
★ 1.9k
What data do you have? Generally, you start with sequencing data, which you need to clean and then map to a reference genome. Then dependin…
Comment: Too many unpaired forward reads found by Trimmomatic
by
GenoMax
142k
> when I didn't provide the adapter file Still see the file here `ILLUMINACLIP:./NexteraPE-PE.fa:2:30:10 `, unless that is an empty file.
Comment: Too many unpaired forward reads found by Trimmomatic
by
SilhouetteQ
• 0
Interestingly, when I didn't provide the adapter file, the number of unpaired forward reads was significantly reduced: TrimmomaticPE…
Comment: Alignment of samples with spike-in
by
GenoMax
142k
> but then if you only allow to map uniquely mapped reads, you are losing spike-in information, How so? Spike-in's are generally unique s…
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
While there is no timeout by default on the `get` operation, you may want to set a higher value and see if that helps, since there is a lar…
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
The " missing is because of a copy-paste error in the post.. I know wget but my tool is entirely in python. I really don't understand why i…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.8k
and if I use the command as such: ``` umi_tools extract --extract-method=regex --error-correct-cell \ --bc-pattern2='(?P…
Comment: UMI-Tools knee-method has great influence on the results of white list
by
i.sudbery
19k
No, UMI-tools won't work this out automatically, you'll need to either switch read1 and read2 or use the new `--read2-only` which is curren…
Comment: Correlation Analysis
by
manaswwm
▴ 510
If your *gene_corr* data frame contains one gene instead of all genes, then the correlation would be per gene. If your *gene_corr* data fra…
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