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Limit : this week
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189 results • Page
3 of 4
Sort: Votes
Rank
Views
Votes
Replies
0
votes
0
replies
94
views
Empty table plot using plotGseaTable()
FGSEA
16 hours ago by
Chris
▴ 260
0
votes
0
replies
94
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
2 days ago by
meck
• 0
0
votes
0
replies
121
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 2 days ago by
Ram
43k • written 2 days ago by
Oscar
▴ 10
0
votes
1
reply
198
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 2 days ago by
GenoMax
142k • written 2 days ago by
mgranada3
▴ 30
0
votes
1
reply
581
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 2 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
0
replies
92
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
2 days ago by
James
▴ 10
0
votes
1
reply
267
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 2 days ago by
Scooter
▴ 280 • written 8 days ago by
avocado123
• 0
0
votes
1
reply
109
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 15 hours ago by
bk11
★ 2.4k • written 17 hours ago by
Rob
▴ 170
0
votes
0
replies
94
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
2 days ago by
Vijith
▴ 30
0
votes
0
replies
83
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
Use of annotation of integrated Seurat object in single sample
Seurat
2 days ago by
Bine
▴ 60
0
votes
5
replies
236
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 12 hours ago by
chrchang523
10k • written 21 hours ago by
curious
▴ 750
0
votes
1
reply
216
views
Subsetting and merging back Seurat Object brings different results
Seurat
2 days ago by
Bine
▴ 60
0
votes
1
reply
183
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 12 hours ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
0
replies
89
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
4 days ago by
Sara
▴ 30
0
votes
1
reply
137
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 5 days ago by
GenoMax
142k • written 5 days ago by
Winter
• 0
0
votes
2
replies
26
views
creating batch colum for batch correction
batch
correction
combat
just now by
Expert
▴ 10
0
votes
5
replies
371
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 6 days ago by
Istvan Albert
100k • written 10 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
99
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 1 day ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
124
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 1 day ago by
Ram
43k • written 2 days ago by
4r-rtg
• 0
0
votes
1
reply
97
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 9 hours ago by
GenoMax
142k • written 16 hours ago by
Ximena
• 0
0
votes
1
reply
773
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 1 day ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
0
replies
96
views
vg call vs vg surject
vg
variation
graphs
updated 5 days ago by
GenoMax
142k • written 5 days ago by
aliraza3119
• 0
0
votes
1
reply
497
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 1 day ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
274
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 5 days ago by
trausch
★ 1.9k • written 21 days ago by
zec018
• 0
0
votes
2
replies
153
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
0
replies
107
views
LEfSe
LEfSe
5 days ago by
benkosta
• 0
0
votes
1
reply
139
views
Provean help
variant
Provean
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Arun Sai Kumar
• 0
0
votes
1
reply
73
views
HCL database download
database
HCL
human
updated 9 hours ago by
GenoMax
142k • written 10 hours ago by
sooni
▴ 20
0
votes
1
reply
141
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 1 day ago by
anovak
▴ 120 • written 1 day ago by
Hang
• 0
0
votes
1
reply
335
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Jesse
▴ 740 • written 14 days ago by
yifangt86
▴ 60
0
votes
2
replies
158
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
5 days ago by
Lluís R.
★ 1.2k
0
votes
7
replies
510
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 1 day ago by
LChart
3.9k • written 4 days ago by
kl
▴ 10
0
votes
2
replies
149
views
Downloading older version of a tool
Alignment
tools
8 hours ago by
Ruqaiya
• 0
0
votes
1
reply
180
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 1 day ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
0
votes
2
replies
684
views
homer not configured properly
Homer
makeTagDirectory
updated 1 day ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
0
votes
1
reply
542
views
HOMER on AWS
HOMER
updated 1 day ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
99
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
0
votes
0
replies
81
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 day ago by
Amos Bairoch
▴ 120
0
votes
5
replies
290
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 1 day ago by
Mohamed Abderrahmane
▴ 20 • written 5 days ago by
matteo.levorato
• 0
0
votes
1
reply
98
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 7 hours ago by
Ram
43k • written 15 hours ago by
SHN
▴ 40
0
votes
5
replies
262
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 1 day ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
JH
• 0
0
votes
0
replies
114
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
67
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 7 hours ago by
Ram
43k • written 15 hours ago by
deepak180001
• 0
0
votes
1
reply
92
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 7 hours ago by
Ram
43k • written 17 hours ago by
Valentina
• 0
0
votes
1
reply
94
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 hours ago by
Thanujay S
• 0 • written 21 hours ago by
yahn
• 0
0
votes
1
reply
210
views
Finding batch and outlayers
Pca
updated 5 days ago by
christopher medway
▴ 460 • written 5 days ago by
Tigran
• 0
0
votes
0
replies
81
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
1 day ago by
rustykb
▴ 20
0
votes
0
replies
25
views
Homer motif analysis
Homer
3 hours ago by
daffodil
▴ 10
0
votes
0
replies
20
views
Help with DGEList function
bioinformatics
2 hours ago by
Natali
• 0
189 results • Page
3 of 4
Recent Votes
Answer: Searching for gene in multiple genomes
Comment: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
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• 0
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▴ 40
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Recent Replies
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…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
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