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310 results • Page
1 of 7
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Rank
Views
Votes
Replies
0
votes
1
reply
61
views
Unable to install HorvathMammalMethylChip40manifest packages
r
programming
updated 3 hours ago by
ATpoint
77k • written 4 hours ago by
Nibedita
• 0
0
votes
0
replies
56
views
TEtranscripts Tool in Galaxy
RNAseq
Transposable_Elements
TE_Transcripts
11 hours ago by
gorizwango
▴ 30
0
votes
0
replies
54
views
rMats Run Does Not Generate More Than One Output Row Per File
Singularity
rMats
sif
14 hours ago by
Y
• 0
1
vote
1
reply
107
views
Imputation server failing to see samples in VCF files
imputation
VCF
updated 17 hours ago by
Ram
40k • written 20 hours ago by
Ben
• 0
0
votes
1
reply
126
views
Issues with featureCounts
featurecounts
rna-seq
differential-expression
updated 16 hours ago by
Ram
40k • written 1 day ago by
Aime
• 0
0
votes
1
reply
115
views
Quality Control of VCFs that used different genotyping arrays
bcftools
VCF
updated 18 hours ago by
bk11
★ 1.3k • written 1 day ago by
Shane
• 0
1
vote
4
replies
249
views
How to perform hypothesis testing on contingency tables and compare with the null distribution?
hypothesis-testing
contingency-table
17 hours ago by
RK
• 0
0
votes
1
reply
112
views
QC of genetic data
PLINK
updated 17 hours ago by
bk11
★ 1.3k • written 1 day ago by
kl
▴ 10
1
vote
3
replies
170
views
differences between trajectories in conditions with Monocle3 or other tools
trajectory
scRna-seq
monocle3
single-cell
updated 14 hours ago by
Amitm
★ 2.2k • written 1 day ago by
Chironex
▴ 40
0
votes
0
replies
82
views
Can optimal cofactors for arcsinh transformation be calculated in parallel?
parallel
R
flowcytometry
flowCore
flowVS
1 day ago by
gmiller
• 0
0
votes
0
replies
82
views
Is the concept of a cofactor in an arcsinh transformation specific to Flow Cytometry?
FlowCytometry
flowCore
FlowVS
1 day ago by
gmiller
• 0
1
vote
1
reply
151
views
Comparing multiple RNASeq studies
RNASeq
updated 1 day ago by
Zhenyu Zhang
▴ 980 • written 1 day ago by
Luke
▴ 10
0
votes
1
reply
125
views
Issue with merging in plink and eigensoft.
Eigensoft
Eigenstrat
Plink
updated 1 day ago by
bk11
★ 1.3k • written 1 day ago by
Jd
• 0
3
votes
3
replies
207
views
Clustering in single cell
seurat
single-cell
1 day ago by
Chris
▴ 200
0
votes
0
replies
97
views
Convert from limma voom normalized matrix each gene to high/low
limma-voom
RNA-SEQ
updated 1 day ago by
Ram
40k • written 1 day ago by
Manuel Sokolov Ravasqueira
▴ 100
3
votes
15
replies
462
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
1 day ago by
ella
• 0
0
votes
0
replies
101
views
Guide for ICD-10 to EFO conversion?
icd10
efo
2 days ago by
optimistsso4co3
▴ 100
0
votes
0
replies
102
views
Software for chimera detection of amplicon (e.g. 16S) nanopore reads
chimera
nanopore
amplicon
2 days ago by
rob_DNA
▴ 10
1
vote
3
replies
239
views
comparision of umap single cell
single-cell
1 day ago by
synat.keam
▴ 80
0
votes
0
replies
116
views
tensorQTL interaction issue
genomics
eqtl
genetics
qtl
2 days ago by
Solal
• 0
1
vote
5
replies
372
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R
edgeR
limma
RNA-seq
updated 1 day ago by
LChart
3.4k • written 2 days ago by
svlachavas
▴ 780
1
vote
5
replies
275
views
CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
R
Picard
CollectRnaSeqMetrics
updated 1 day ago by
Ram
40k • written 2 days ago by
camillab.
▴ 140
8
votes
5
replies
320
views
Frustrated with DEA results
microarray
differential-expression
updated 1 day ago by
dsull
★ 4.8k • written 2 days ago by
jopadrosa
• 0
0
votes
0
replies
112
views
Select minimum set of SNPs from VCF file to identify a individual
selection
SNP
2 days ago by
Bioxbio
• 0
0
votes
0
replies
95
views
How to obtain de pvalue of my DMRs using Bumphunter function from minfi
DMRs
2 days ago by
Irene
• 0
1
vote
4
replies
220
views
How to filter vcf file by MAF using bcftools?
bcftools
vcf
updated 2 days ago by
Ram
40k • written 2 days ago by
_quantum_girl_
▴ 10
0
votes
3
replies
203
views
What is the correct procedure to generate a consensus bacterial sequence?
consensus
samtools
illumina
fastq
22 hours ago by
marongiu.luigi
▴ 690
0
votes
2
replies
179
views
Detect STRs in illumina library
repeats
annotation
STR
2 days ago by
kirillkirilenko
▴ 20
1
vote
3
replies
318
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
1 day ago by
dalibenam64
• 0
0
votes
4
replies
227
views
Sequence quality drops in the 3' end of the left sequence in paired end. What could be the cause?
sequencing
updated 3 days ago by
GenoMax
134k • written 3 days ago by
eggrandio
▴ 40
15
votes
16
replies
719
views
ncbi error report log for validate fastq issue
sra-tools
updated 2 days ago by
GenoMax
134k • written 3 days ago by
1769mkc
★ 1.1k
0
votes
3
replies
177
views
Bug of vg surject
vg
updated 3 days ago by
Jordan M Eizenga
▴ 360 • written 3 days ago by
Qi
• 0
0
votes
1
reply
154
views
GO ENRICHMENT ANALYSIS- DESEQ
GO
updated 3 days ago by
Basti
★ 1.7k • written 3 days ago by
oduduabasi.isaiah
• 0
0
votes
6
replies
333
views
Troubles launch IGV on Linux(Debian)
IGV
1 day ago by
PoscaXVIII
• 0
0
votes
1
reply
139
views
DESeq2 error - converting result object into dataframe
R
DESeq2
Shiny
updated 3 days ago by
Ram
40k • written 3 days ago by
shasabhi1
• 0
0
votes
1
reply
134
views
Calculating haplotype and nucleotide diversity with deep amplicon sequencing data
haplotype
diversity
Pegas
Arlequin
HTS_data
3 days ago by
deorugz
• 0
3
votes
3
replies
2.2k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 3 days ago by
Ram
40k • written 2.0 years ago by
Anand
▴ 40
0
votes
0
replies
102
views
How to remove chimera from 16S Sanger contigs
sanger-sequencing
chimera
uchime
updated 3 days ago by
Ram
40k • written 3 days ago by
eimanpharmacist
▴ 20
1
vote
5
replies
219
views
bcftools error merging two VCFs: REF prefixes differ
bcftools
VCF
3 days ago by
Shane
• 0
0
votes
2
replies
687
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
2 days ago by
kat.bi
• 0
0
votes
2
replies
203
views
how to create a loop in R
R
offtopic
updated 3 days ago by
Ram
40k • written 4 days ago by
mthm
▴ 50
0
votes
1
reply
164
views
GO analysis after DESeq2
GO
updated 4 days ago by
Ram
40k • written 4 days ago by
oduduabasi.isaiah
• 0
3
votes
2
replies
194
views
Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
methylation
DMR
updated 4 days ago by
Basti
★ 1.7k • written 4 days ago by
epianalysis
• 0
0
votes
1
reply
148
views
Download an example of fully-imputed VCF files ?
VCF
impute
updated 4 days ago by
barslmn
★ 1.8k • written 4 days ago by
Ben
• 0
0
votes
0
replies
120
views
How to annotate BED for tissue expression?
BED
annotation
4 days ago by
Fabio_bie88
• 0
0
votes
1
reply
1.7k
views
error when running local chlorop1.1
chlorop
updated 4 days ago by
Ram
40k • written 7.3 years ago by
gerrychang1985
▴ 40
0
votes
6
replies
277
views
gene correlations in between two groups
gene-expression
correlation
3 days ago by
biology_inform
▴ 40
0
votes
1
reply
123
views
Running Ibex on both BCR chains?
BCR
ibex
single-cell
updated 4 days ago by
Ram
40k • written 5 days ago by
actinia94
• 0
2
votes
9
replies
472
views
Calculation of TMB on gene level
genomics
updated 4 days ago by
svp
▴ 590 • written 5 days ago by
smrutimayipanda
▴ 20
0
votes
0
replies
111
views
Spike-in normalization in ATAC-Seq with DiffBind
ATAC-Seq
spike-in
DiffBind
5 days ago by
frueher
• 0
310 results • Page
1 of 7
Recent Votes
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
Answer: TPM RNA-seq data for differential expression analysis
A: Error When Installing Emboss
Answer: Subclustering of intergated cells from scRNA-seq data
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Recent Replies
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data
by
fifty_fifty
▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
Comment: How to get the gft file to run velocyto for velocity analysis?
by
Chris
▴ 200
Yes, thank you! I figured it out but I got an error: velocyto run10x -m Hg38_rmsk.gtf WT/outs /cellranger/reference/refdata-cellranger…
Comment: How to get the gft file to run velocyto for velocity analysis?
by
bk11
★ 1.3k
You can get from here- [UCSC][1]. Just click on get output botton. [1]: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=611454127_NtvlaW…
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