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396 results • Page 4 of 8
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NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 25 days ago by 43k • written 7.0 years ago by • 0
0
votes
1
reply
201
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 19 days ago by • 0 • written 20 days ago by • 0
0
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1
reply
119
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consensus sequence calling
consensus
updated 20 hours ago by ★ 2.4k • written 1 day ago by • 0
0
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0
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2.7k
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Comparing lists generated by Counter() and .most_common() for AA seqs
python amino-acid
updated 27 days ago by 43k • written 9.9 years ago by ★ 2.7k
0
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1
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305
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 26 days ago by 142k • written 26 days ago by • 0
0
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0
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231
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 25 days ago by 43k • written 25 days ago by ▴ 10
0
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0
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1.3k
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which value from ruvadj in missMethyl can present methylation status
R RUV methylation missmethyl batch-effect
updated 27 days ago by 43k • written 6.0 years ago by ▴ 20
0
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0
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108
views
Cellphonedb results
cpdb visulization cellphonedb
7 days ago by piotto ▴ 20
0
votes
2
replies
307
views
Annovar using R package
Annovar gnomAD R
18 days ago by DKA ▴ 40
0
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0
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1.8k
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Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect RNA-Seq Differential-Expression
updated 27 days ago by 43k • written 7.2 years ago by ▴ 270
0
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1
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555
views
HOMER on AWS
HOMER
updated 11 days ago by • 0 • written 2.2 years ago by ★ 1.4k
0
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0
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899
views
Advice on group specific condition effect and model matrix in deseq2
deseq2 batch-effect
updated 28 days ago by 43k • written 4.1 years ago by ▴ 330
0
votes
1
reply
167
views
tbtool
tbtool
updated 21 days ago by 43k • written 21 days ago by • 0
0
votes
0
replies
171
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
19 days ago by Aspire ▴ 330
0
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0
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195
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
26 days ago by P. • 0
0
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0
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1.8k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq gene-expression-matrix correlation R
updated 27 days ago by 43k • written 6.3 years ago by ▴ 30
0
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5
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255
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 6 days ago by 21k • written 6 days ago by • 0
0
votes
0
replies
149
views
Trouble converting tfam and tped to map and ped files
plink ped tfam tped map
4 days ago by Samantha • 0
0
votes
0
replies
211
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
26 days ago by synat.keam ▴ 100
0
votes
0
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147
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification Metagenomics Krona Kraken2
4 days ago by Aytaç • 0
0
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0
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206
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
24 days ago by Nitin • 0
0
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0
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601
views
Differential accessibility using DiffBinf
diffbind
15 days ago by Shloka • 0
0
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0
replies
137
views
Add geno header to VariantAnnotation objects
nichenet scRNA-seq
28 days ago by QX • 0
0
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1
reply
182
views
unable to get feature count results
featureCounts
updated 13 days ago by 43k • written 14 days ago by • 0
0
votes
1
reply
224
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How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 28 days ago by ★ 2.4k • written 28 days ago by • 0
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5
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6.0k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 24 days ago by • 0 • written 6.5 years ago by ▴ 30
0
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0
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1.5k
views
minifi for RRBS
rrbs batch-effect methylation
updated 27 days ago by 43k • written 7.2 years ago by ★ 2.9k
0
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2
replies
210
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
1 day ago by analyst ▴ 50
0
votes
2
replies
288
views
Extracting mutation status from MAF files - TCGA
TCGA maf mutation
updated 1 day ago by ★ 1.2k • written 10 days ago by • 0
0
votes
2
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2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 25 days ago by 43k • written 7.1 years ago by • 0
0
votes
1
reply
416
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 25 days ago by 43k • written 20 months ago by • 0
0
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0
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158
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq ArchR
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
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133
views
Mitogenomes gap closure and making circular genome
gapclosure Mitogenomes validation circulargenome
8 days ago by KHURRAM SHAHZAD • 0
0
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0
replies
142
views
vcf procesing for ML antigen prediction
formats vcf fastaq HLA_imputation HLA_typing
10 days ago by Javier • 0
0
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0
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154
views
Automated internal stop codon checker
ORF stopcodon internal virus
29 days ago by Balazs Horvath ▴ 10
0
votes
4
replies
169
views
Galaxy StringTie error
stringtie galaxy
2 hours ago by trkfs • 0
0
votes
2
replies
179
views
Phasing a mixture of two individuals' DNA with long reads
long-reads phasing
6 days ago by njornet ▴ 20
0
votes
2
replies
462
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
25 days ago by Ashok • 0
0
votes
0
replies
117
views
The concept of co-occurrence network structure
co-occurence microbiome network
20 days ago by ohtang7 ▴ 40
0
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1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva batch-effect
updated 26 days ago by 43k • written 6.2 years ago by ▴ 40
0
votes
2
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419
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
25 days ago by Ashok • 0
0
votes
1
reply
529
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 18 days ago by • 0 • written 5 months ago by • 0
0
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0
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1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 25 days ago by 43k • written 4.1 years ago by • 0
0
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0
replies
208
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
25 days ago by enferdeflame • 0
0
votes
0
replies
134
views
Modify plot R mtDNA indel
plot mtDNA R
10 days ago by marco.barr ▴ 110
0
votes
1
reply
192
views
Differential Accessibility
DiffBind
updated 14 days ago by 43k • written 14 days ago by • 0
0
votes
1
reply
269
views
creating batch colum for batch correction
batch-correction combat
8 days ago by Expert ▴ 10
0
votes
0
replies
115
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 20 days ago by 43k • written 21 days ago by • 0
0
votes
0
replies
223
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 24 days ago by 43k • written 25 days ago by • 0
0
votes
0
replies
103
views
Help with finding conferences in immuno-informatics/virology
virology conferences immunology
21 days ago by manaswwm ▴ 510
396 results • Page 4 of 8
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A: How to get read counts on transcript level using featurecounts?
Answer: Vcf file sorting
Answer: How to interpret infinite odds ratio?
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Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
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Recent Replies
Comment: How to access GWAVA software of data by GenoMax 142k
Please email the author (grsr at ebi.ac.uk) and let them know that the link above is not available.
Comment: CNVKIT - unable to produce scatter and diagram pdfs by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: CNVkit for somatic copy number detection by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Comment: CNVkit for somatic copy number detection by Anitha • 0
The normal samples is pooled into single reference for cohort. In this I have a doubt, here the normal sample referred as sample which took…
Answer: Overlapping Ranges within Granges object by ATpoint 82k
There is no one-hit function in GenomicRanges, but you can stick something together using a combination of `findOverlaps` to first find ove…
Comment: Galaxy StringTie error by trkfs • 0
Hi, I did not encounter any " \ - " characters in the fastq input files, and it doesn't seem to be present in any other files either. Thank…
Comment: How to interpret infinite odds ratio? by Lukas • 0
Thanks you for your answer. But according that links interpretation of inf odds ratio is up to hypothesis of the researcher.So my solution …
Comment: How to access GWAVA software of data by nonaddldy ▴ 10
Not found in https://ftp.sanger.ac.uk/resources/software/gwava/ ![][1] [1]: /media/images/f69695ec-e047-44f6-95ce-cd4edf1c
Comment: How to access GWAVA software of data by nonaddldy ▴ 10
https://www.sanger.ac.uk/tool/gwava/
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by IdaHao0921 • 0
The species I study is not a model species, VQSR can not be applied here. I already used gatk hard-filtering. I mean, after hard-filtering,…
Answer: Overlapping Ranges within Granges object by Alex Reynolds 35k
If you're not tied to Granges, you could use `bedmap --fraction-both 0.1` to require at least 10% overlap between reference and map regions…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
By doing some online search, I tried installing one module `cpan Bio::DB::Fasta` and it is running like a never-ending installation process…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Vijith ▴ 30
I have tried installing AGAT. But it failed the tests. …
Comment: BWA alignment by ATpoint 82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation by ATpoint 82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
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