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464 results • Page
3 of 10
Sort: Votes
Rank
Views
Votes
Replies
1
vote
2
replies
254
views
alignment result
RNA-seq
samtools
hisat2
9 days ago by
ahmad.sajad4541
• 0
1
vote
2
replies
337
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 19 days ago by
Istvan Albert
100k • written 20 days ago by
Jiang
• 0
1
vote
1
reply
203
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
19 days ago by
CTLong
▴ 110
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva
batch-effect
RRBS
updated 17 days ago by
Ram
43k • written 7.2 years ago by
mrodrigues.fernanda
▴ 50
1
vote
2
replies
242
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
2 days ago by
rianna.collins
• 0
1
vote
1
reply
183
views
Failed to download data from EBI with ascp
EBI
aspera
updated 23 days ago by
GenoMax
142k • written 23 days ago by
biock
▴ 60
1
vote
1
reply
246
views
Retrieve a % coverage for each transcript
RNA-seq
updated 17 days ago by
Ram
43k • written 17 days ago by
jammydodger123456
▴ 40
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 17 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
2
replies
225
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
Ravita
• 0
1
vote
1
reply
228
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 3 days ago by
Ram
43k • written 4 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
260
views
permutation test in edgeR
rna-seq
edgeR
updated 12 days ago by
Gordon Smyth
★ 7.1k • written 26 days ago by
Netanel
• 0
1
vote
4
replies
833
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
24 days ago by
Hyper_Odin
▴ 310
1
vote
2
replies
940
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 29 days ago by
Ram
43k • written 24 months ago by
ved_vyas
▴ 20
1
vote
4
replies
358
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
29 days ago by
diqixiaoyaoer
▴ 10
1
vote
0
replies
1.1k
views
interpretation of trajectory and batch effect
monocle3
batch-effect
trajectory
updated 26 days ago by
Ram
43k • written 3.5 years ago by
tushard1987
▴ 10
1
vote
3
replies
384
views
Ensembl gene id conversion
biomart
ensembl
updated 18 days ago by
ATpoint
82k • written 20 days ago by
naveedhasan2000
• 0
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 2 days 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
1
vote
3
replies
219
views
Odd alignment question/finding
Alignment
updated 1 day ago by
barslmn
★ 2.1k • written 2 days ago by
poordumbsillyidiot
• 0
1
vote
1
reply
477
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 26 days ago by
chrchang523
10k • written 26 days ago by
dsbusiness135
▴ 10
1
vote
0
replies
165
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
23 days ago by
eebloom
▴ 80
1
vote
1
reply
441
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 13 days ago by
Gordon Smyth
★ 7.1k • written 16 days ago by
Chris
▴ 260
1
vote
3
replies
267
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
11 days ago by
WouterDeCoster
47k
1
vote
1
reply
197
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 18 days ago by
dsull
★ 6.0k • written 18 days ago by
niruf
• 0
1
vote
0
replies
679
views
Conditions for valid batch effect correction
r
batch-effect
updated 17 days ago by
Ram
43k • written 5.2 years ago by
Sebastian Hesse
▴ 340
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 19 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
1
vote
8
replies
469
views
Downsampling fastq file
downsample
fastq
4 days ago by
marco.barr
▴ 90
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq
batch-effect
SNP
updated 16 days ago by
Ram
43k • written 7.5 years ago by
oselm
▴ 50
0
votes
0
replies
169
views
Analyzing differentially methylated regions from Nanopore long read data?
Long-read-sequencing
methylation
updated 29 days ago by
Ram
43k • written 7 weeks ago by
Arton
• 0
0
votes
0
replies
132
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
4 days ago by
Jacob
• 0
0
votes
2
replies
301
views
bam merging for archaic samples
samtools
bam
updated 13 days ago by
Ram
43k • written 14 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
83
views
Imputation advice
imputation
12 days ago by
kl
▴ 10
0
votes
3
replies
302
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
26 days ago by
Jeyong
• 0
0
votes
0
replies
48
views
GRCh38.gmap file
gnomix
gmap
7 hours ago by
lorena9132
• 0
0
votes
0
replies
155
views
CIBERSORT deconvolution by using long read sequencing data
long-read-sequencing
CIBERSORT
updated 29 days ago by
Ram
43k • written 29 days ago by
IVORY
• 0
0
votes
0
replies
226
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
5 days ago by
SSSJec
• 0
0
votes
0
replies
738
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
0
votes
0
replies
155
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
9 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
879
views
freebayes calls presumably homozygous variants as heterozygotes
SNP
freebayes
variant-call
genotyping
updated 29 days ago by
virginia.baraja
• 0 • written 3.1 years ago by
johanna.pieplow
• 0
0
votes
0
replies
111
views
Databases with GoF (Gain of Function) annotations.
gof
lof
gain-of-function
25 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
78
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
0
replies
388
views
Differential accessibility using DiffBinf
diffbind
5 days ago by
Shloka
• 0
0
votes
1
reply
160
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 12 days ago by
Ram
43k • written 12 days ago by
Cameron.walker9900
• 0
0
votes
0
replies
212
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 12 days ago by
Ram
43k • written 12 days ago by
Oak
▴ 10
0
votes
1
reply
141
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
159
views
FreeBayes detection capacity
reads
freebayes
long
19 days ago by
quentinperriere
• 0
0
votes
2
replies
224
views
How to update R on ubuntu
installation
update
R
apt-get
5 days ago by
Bosberg
▴ 50
0
votes
1
reply
112
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 15 hours ago by
Ram
43k • written 1 day ago by
Valentina
• 0
0
votes
3
replies
216
views
Software to separate reads from different individuals
software
development
nanopore
updated 5 days ago by
GenoMax
142k • written 5 days ago by
njornet
▴ 20
0
votes
0
replies
47
views
Help with DGEList function
DGEList
R
updated 2 hours ago by
Ram
43k • written 10 hours ago by
Natali
• 0
464 results • Page
3 of 10
Recent Votes
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Comment: RNA velocity for smart-seq2 dataset
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dsull
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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…
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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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