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190 results • Page
4 of 4
Sort: Rank
Rank
Views
Votes
Replies
3
votes
2
replies
298
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 days ago by
i.sudbery
19k • written 8 days ago by
vanbelj
▴ 40
0
votes
0
replies
122
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 5 days ago by
dariober
14k • written 6 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
302
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Francesco
▴ 10
0
votes
0
replies
139
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
6 days ago by
tnminh89
▴ 10
0
votes
0
replies
144
views
Filter low express genes in microarray data
microarray
6 days ago by
Chris
▴ 260
0
votes
1
reply
335
views
absolute path for symbolic links in Snakefile
Snakemake
updated 6 days ago by
Jesse
▴ 740 • written 15 days ago by
yifangt86
▴ 60
0
votes
2
replies
357
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment
gaps
updated 6 days ago by
Jesse
▴ 740 • written 9 days ago by
Broccoli
• 0
1
vote
3
replies
394
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 5 days ago by
Mensur Dlakic
★ 27k • written 7 days ago by
O.rka
▴ 710
4
votes
2
replies
304
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
5 days ago by
pairedttest
▴ 10
1
vote
7
replies
504
views
gvcf joint calling
WES
GATK
VCF
gVCF
6 days ago by
zihanss
• 0
0
votes
3
replies
389
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
4 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
2
replies
340
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
6 days ago by
Francesco
▴ 10
1
vote
7
replies
503
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 5 days ago by
bk11
★ 2.4k • written 9 days ago by
starswillfade
▴ 10
2
votes
5
replies
369
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
5 days ago by
analyst
▴ 30
1
vote
3
replies
385
views
PCA plot
DESeq2
PCAplot
updated 5 days ago by
LauferVA
4.2k • written 9 days ago by
Aaliya
▴ 10
5
votes
5
replies
560
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 22 hours ago by
Mbofire
• 0 • written 9 days ago by
Ming Tommy Tang
★ 3.9k
1
vote
1
reply
170
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
3 days ago by
heelpPlease
• 0
5
votes
4
replies
365
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
2 days ago by
Estevão
• 0
2
votes
4
replies
283
views
from row count to tpm
tpm
row-count
normalization
updated 4 days ago by
Ram
43k • written 12 days ago by
michelafrancesconi9
▴ 20
1
vote
8
replies
469
views
Downsampling fastq file
downsample
fastq
4 days ago by
marco.barr
▴ 90
0
votes
10
replies
512
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 4 days ago by
i.sudbery
19k • written 12 days ago by
Patadu94
• 0
2
votes
11
replies
910
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 5 days ago by
jkbonfield
★ 1.2k • written 17 days ago by
me
• 0
1
vote
6
replies
328
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 1 day ago by
GenoMax
142k • written 19 days ago by
eebloom
▴ 80
1
vote
0
replies
186
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
2 days ago by
carlopecoraro2
★ 2.5k
1
vote
2
replies
277
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
1 day ago by
eebloom
▴ 80
0
votes
3
replies
337
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 5 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 14 hours ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
2 days ago by
eebloom
▴ 80
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 2 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 5 days ago by
Medhat
9.7k • written 24 months ago by
Vitor1
▴ 120
2
votes
5
replies
929
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 5 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 1 day ago by
ST
• 0 • written 2.2 years ago by
Federico
• 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
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
5 days ago by
anna
▴ 20
16
votes
12
replies
7.3k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 1 day ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 1 day ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 1 day ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 5 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 4 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 6 hours ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
190 results • Page
4 of 4
Recent Votes
Answer: Design matrix Differential expression analysis
A: extract dendrogram cluster from pheatmap
extract dendrogram cluster from pheatmap
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Comment: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
Answer: RNA velocity for smart-seq2 dataset
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★ 1.7k
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drajangirija
• 0
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Recent Replies
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…
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…
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