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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
60
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
filtering
independent
linkage
9 hours ago by
Jautis
▴ 530
0
votes
2
replies
142
views
creating batch colum for batch correction
batch-correction
combat
updated 11 hours ago by
Ram
43k • written 19 hours ago by
Expert
▴ 10
0
votes
0
replies
66
views
Help with DGEList function
DGEList
R
updated 11 hours ago by
Ram
43k • written 19 hours ago by
Natali
• 0
0
votes
0
replies
67
views
Homer motif analysis
Homer
20 hours ago by
daffodil
▴ 10
0
votes
1
reply
110
views
HCL database download
database
HCL
human
updated 1 day ago by
GenoMax
142k • written 1 day ago by
sooni
▴ 20
0
votes
0
replies
90
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 1 day ago by
Ram
43k • written 1 day ago by
deepak180001
• 0
0
votes
1
reply
135
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Ximena
• 0
0
votes
1
reply
132
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 1 day ago by
Ram
43k • written 1 day ago by
Valentina
• 0
0
votes
6
replies
328
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
Erina
• 0
0
votes
1
reply
119
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Lada
▴ 30
0
votes
0
replies
94
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
1 day ago by
Emilie
• 0
0
votes
0
replies
91
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
1 day ago by
Javier
• 0
0
votes
1
reply
174
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 23 hours ago by
Thanujay S
• 0 • written 1 day ago by
yahn
• 0
0
votes
0
replies
88
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
1 day ago by
mikemakaveli1
• 0
0
votes
0
replies
90
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
2
replies
151
views
Raw counts using stringtie
stringtie
RNA-seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
86
views
Modify plot R mtDNA indel
plot
mtDNA
R
1 day ago by
marco.barr
▴ 90
0
votes
0
replies
190
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
1 day ago by
NorbertK
• 0
0
votes
2
replies
186
views
Downloading older version of a tool
Alignment
tools
1 day ago by
Ruqaiya
• 0
0
votes
0
replies
103
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
1 day ago by
rustykb
▴ 20
3
votes
5
replies
224
views
Generating mpileup file using samtools
mpileup
samtools
updated 1 day ago by
Joe
21k • written 1 day ago by
Ruqaiya
• 0
2
votes
3
replies
241
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 1 day ago by
dthorbur
★ 1.9k • written 1 day ago by
Vijith
▴ 30
0
votes
0
replies
121
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
2 days ago by
Jeyong
• 0
0
votes
0
replies
113
views
Empty table plot using plotGseaTable()
FGSEA
1 day ago by
Chris
▴ 260
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 2 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
177
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
2 days ago by
dtnondorf
• 0
0
votes
1
reply
203
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 2 days ago by
Chris Dean
▴ 390 • written 2 days ago by
sovrappensiero
▴ 90
2
votes
6
replies
325
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
2 days ago by
Qroid
▴ 40
0
votes
1
reply
143
views
Provean help
variant
Provean
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Arun Sai Kumar
• 0
0
votes
0
replies
96
views
Use of annotation of integrated Seurat object in single sample
Seurat
2 days ago by
Bine
▴ 60
0
votes
1
reply
217
views
Subsetting and merging back Seurat Object brings different results
Seurat
2 days ago by
Bine
▴ 60
1
vote
1
reply
134
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 90
0
votes
0
replies
84
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
2 days ago by
Rhiannon
• 0
0
votes
0
replies
95
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
3 days ago by
Vijith
▴ 30
0
votes
0
replies
96
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
3 days ago by
James
▴ 10
0
votes
1
reply
584
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 3 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
222
views
Odd alignment question/finding
Alignment
updated 1 day ago by
barslmn
★ 2.1k • written 3 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
203
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 3 days ago by
GenoMax
142k • written 3 days ago by
mgranada3
▴ 30
0
votes
0
replies
95
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
3 days ago by
meck
• 0
0
votes
0
replies
124
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 3 days ago by
Ram
43k • written 3 days ago by
Oscar
▴ 10
0
votes
1
reply
143
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 3 days ago by
Ram
43k • written 3 days ago by
ernestine.kubi
• 0
0
votes
0
replies
105
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
3 days ago by
VITALA
• 0
1
vote
2
replies
244
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
3 days ago by
rianna.collins
• 0
0
votes
1
reply
180
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Edmond
• 0
0
votes
0
replies
142
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
4 days ago by
O.rka
▴ 710
0
votes
1
reply
620
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 4 days ago by
Ram
43k • written 4 days ago by
Dr Huma Naz
• 0
0
votes
5
replies
365
views
Telescope issue
Telescope
RNA-seq
updated 3 days ago by
GenoMax
142k • written 4 days ago by
eleven11
• 0
1
vote
1
reply
230
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 4 days ago by
Ram
43k • written 4 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
285
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
3 days ago by
Nafi
• 0
1
vote
3
replies
278
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 4 days ago by
GenoMax
142k • written 4 days ago by
jeffrey.maurer.informatics
• 0
1,000 results • Page
1 of 20
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Popular Question
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psm
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Recent Replies
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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