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13,541 results • Page
2 of 271
Sort: Rank
Rank
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Votes
Replies
0
votes
1
reply
251
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
1
vote
4
replies
335
views
Segmentation error while using a tool
smalt
updated 2 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
Ruqaiya
• 0
0
votes
1
reply
202
views
Help with DGEList function
DGEList
R
updated 1 day ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
0
votes
0
replies
145
views
Homer motif analysis
Homer
3 days ago by
daffodil
▴ 10
0
votes
3
replies
245
views
HCL database download
database
HCL
human
4 hours ago by
sooni
▴ 20
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
2 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
289
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 3 days ago by
chrchang523
10k • written 7 days ago by
8armed
▴ 10
0
votes
5
replies
334
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 3 days ago by
chrchang523
10k • written 3 days ago by
curious
▴ 750
0
votes
1
reply
201
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 2 days ago by
Ram
43k • written 3 days ago by
Rob
▴ 170
0
votes
1
reply
195
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Ximena
• 0
0
votes
1
reply
188
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 3 days ago by
Ram
43k • written 3 days ago by
Valentina
• 0
0
votes
6
replies
403
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 3 days ago by
swbarnes2
14k • written 3 days ago by
Erina
• 0
0
votes
2
replies
222
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
19 hours ago by
kalavattam
▴ 190
1
vote
3
replies
273
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
1 day ago by
Lada
▴ 30
1
vote
0
replies
143
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 1 day ago by
zx8754
11k • written 3 days ago by
Emilie
▴ 10
0
votes
0
replies
136
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
3 days ago by
Javier
• 0
0
votes
1
reply
229
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Thanujay S
• 0 • written 3 days ago by
yahn
• 0
0
votes
0
replies
129
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
3 days ago by
mikemakaveli1
• 0
2
votes
2
replies
211
views
Raw counts using stringtie
stringtie
RNA-seq
updated 3 days ago by
GenoMax
142k • written 3 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
129
views
Modify plot R mtDNA indel
plot
mtDNA
R
3 days ago by
marco.barr
▴ 90
0
votes
0
replies
272
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
3 days ago by
NorbertK
• 0
3
votes
2
replies
225
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 2 days ago by
Ram
43k • written 4 days ago by
carolofharvest
▴ 30
11
votes
11
replies
624
views
High Malat-1 expression in single cell data
single-cell
just now by
carolofharvest
▴ 30
0
votes
2
replies
242
views
Downloading older version of a tool
Alignment
tools
3 days ago by
Ruqaiya
• 0
0
votes
0
replies
145
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
3 days ago by
rustykb
▴ 20
1
vote
1
reply
182
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 2 days ago by
Ram
43k • written 4 days ago by
adi.gershon1
• 0
3
votes
5
replies
275
views
Generating mpileup file using samtools
mpileup
samtools
updated 3 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
0
votes
5
replies
354
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 4 days ago by
b.contreras.moreira
▴ 180 • written 4 days ago by
JH
• 0
1
vote
3
replies
284
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Qi
• 0
0
votes
0
replies
135
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
4 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
278
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 3 days ago by
dthorbur
★ 1.9k • written 4 days ago by
Vijith
▴ 30
0
votes
0
replies
145
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
4 days ago by
Jeyong
• 0
0
votes
2
replies
728
views
homer not configured properly
Homer
makeTagDirectory
updated 4 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
255
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 4 days ago by
Alex Reynolds
35k • written 4 days ago by
SJP
• 0
0
votes
0
replies
132
views
Empty table plot using plotGseaTable()
FGSEA
3 days ago by
Chris
▴ 260
0
votes
1
reply
180
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 4 days ago by
anovak
▴ 120 • written 4 days ago by
Hang
• 0
1
vote
3
replies
236
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 4 days ago by
jared.andrews07
★ 16k • written 4 days ago by
yvonneh
▴ 10
3
votes
5
replies
317
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
3 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 4 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
195
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
4 days ago by
dtnondorf
• 0
0
votes
5
replies
381
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 14 hours ago by
Chris Dean
▴ 390 • written 4 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
236
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by
yahn
• 0
2
votes
8
replies
484
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
15 hours ago by
Qroid
▴ 40
0
votes
1
reply
511
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 4 days ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
150
views
Provean help
variant
Provean
updated 4 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
164
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 4 days ago by
bk11
★ 2.4k • written 5 days ago by
Jeol
▴ 20
1
vote
1
reply
170
views
Super ehancers
enhancers
updated 4 days ago by
jared.andrews07
★ 16k • written 5 days ago by
Oburah
• 0
0
votes
6
replies
294
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 3 days ago by
dsull
★ 6.0k • written 4 days ago by
Chen
• 0
5
votes
5
replies
280
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 4 days ago by
atharvakarkare14
▴ 30 • written 5 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
445
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
3 days ago by
eebloom
▴ 80
13,541 results • Page
2 of 271
Recent Votes
A: DESeq2 DEG analysis using different sequencing depth data
Answer: Converting Nebula Genomics Data to 23andMe Format
Answer: Analysis of intronic reads included scRNA-seq data
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
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Comment: High Malat-1 expression in single cell data
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Comment: Highest variable features in single cell data
by
carolofharvest
▴ 30
Thank you. But can we say that this is biologically informative ? If this gene had been detected in excess specifically within a single c…
Answer: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
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• 0
$20,000 for the first Prize?XD
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Why does your question sound like an assignment (if it's not, reformulate it, note you are in no position to give the volunteers here assig…
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54k
Hi, Thank you for your contribution, here is your *free* code review: - This scenario is sort of ideal for a snakemake workflow and I th…
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I'm sorry for any confusion or inconvenience. I'm seeking guidance on which search algorithms are used in the FM-index. I've done extensive…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Hi Daria, I have downloaded pling and the other dependencies as recommended on your github page. I have tried to run the tool a few times …
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by
i.sudbery
19k
The insert size is measured from outermost edge of this read, to the outer most edge of its mate. Like, literally, start_second - start_fir…
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54k
So this is your exam question or assignment? Please understand that posting this here is not doing anyone any good. You are supposed to lea…
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ATpoint
82k
I will say that the proper way is the one that confidently identifies your celltypes. > optimal number of marker genes to consider. T…
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swbarnes2
14k
When everything is the same size, correcting for size is pointless. It doesn't change the numbers much at all.
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by
swbarnes2
14k
What do the alignments look like in IGV?
Comment: HCL database download
by
sooni
▴ 20
I solved the problem! Thanks!
Comment: Gene Specific coverage from WGS data
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Adyasha
• 0
Thank you, here I am giving you some example , suppose I have bam files . 1.bam 2.bam 3.bam 4.bam now I want to see Spike gene coverage in …
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I'm having a problem and I can't find the button to post, how do you post?
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MICOS
▴ 10
Contest question details: **To effectively address the accuracy and efficiency issues of clustering algorithms used for spatial transcript…
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