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116,799 results • Page
2 of 2336
Sort: Rank
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Votes
Replies
0
votes
1
reply
171
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 16 hours ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
0
votes
1
reply
440
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 1 day ago by
GenoMax
142k • written 2 days ago by
tulip
• 0
3
votes
4
replies
396
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 14 hours ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
SHN
▴ 40
4
votes
2
replies
246
views
GRCh38.gmap file
gnomix
gmap
2 days ago by
lorena9132
▴ 10
2
votes
3
replies
811
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 2 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
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
336
views
Segmentation error while using a tool
smalt
updated 3 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
4
replies
255
views
HCL database download
database
HCL
human
updated 10 minutes ago by
GenoMax
142k • written 3 days 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
21 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
144
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
212
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
227
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
12
replies
645
views
High Malat-1 expression in single cell data
single-cell
1 hour ago 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
4 days ago by
rustykb
▴ 20
1
vote
1
reply
184
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 2 days ago by
Ram
43k • written 4 days ago by
adi.gershon1
• 0
3
votes
5
replies
276
views
Generating mpileup file using samtools
mpileup
samtools
updated 4 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
0
votes
5
replies
355
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
729
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
256
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 16 hours ago by
Chris Dean
▴ 390 • written 4 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
237
views
RNA-seq data for deep learning classification
rna-seq
4 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
17 hours ago by
Qroid
▴ 40
0
votes
1
reply
512
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
116,799 results • Page
2 of 2336
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Recent Replies
Comment: trying to count a pattern in my fastq file using bbduk
by
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142k
I don't think you can use N's in `literal=` since the match is literal as the option says. Depending where in the read this pattern is you …
Comment: Repeated testing/data mining in RNA Seq
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I've followed this [vignette][1] [1]: https://tanaylab.github.io/metacells-vignettes/iterative.html Which is the only pipeline that d…
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142k
https://www.biostars.org/u/98332/ : This may be best posted as a new question since you are now running into a problem with tool usage.
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82k
What is your question? See https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html which covers most relevan…
Comment: HCL database download
by
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142k
Please post your solution as an answer.
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Comment: High Malat-1 expression in single cell data
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If rRNA genes have been mistakenly assigned to these genes, could it be expected that the percentage of ribosomal genes(rpl,rps) would be …
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(+1) *"implementing" the method just using base R linear models.*: I find implementing from basic starting point to be one of the best, if …
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by
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★ 2.9k
Mapping rate for bisulfite data is typically worse because of reduced complexity of the sequences. The efficiency will depend on your read …
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▴ 30
In your paper, you mentioned that a normalization value of 0 for Malat1 is also indicative of a low-quality cell. But what if the dropout e…
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carolofharvest
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Thank you. But can we say that this is biologically informative ? If this gene had been detected in excess specifically within a single c…
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$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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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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