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525 results • Page
2 of 11
Sort: Views
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Views
Votes
Replies
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression
RNA-Seq
scRNA-seq
updated 9 days ago by
Ram
43k • written 6.5 years ago by
Eskimo
▴ 120
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA
RNA-Seq
seurat
batch-effect
updated 1 day ago by
Ram
43k • written 5.1 years ago by
akivab2
▴ 110
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
5
replies
1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA
lncRNA
updated 13 days ago by
Ram
43k • written 2.6 years ago by
reza
• 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 13 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
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 3 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
16 days ago by
b.contreras.moreira
▴ 150
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata
functional-annotation
BRAKER
MAKER
updated 17 days ago by
andorjkiss
▴ 40 • written 15 months ago by
javanokendo
▴ 60
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq
deseq2
Differential-Gene-expression
R
updated 9 days ago by
Ram
43k • written 4.9 years ago by
imanbh
• 0
0
votes
0
replies
1.5k
views
RIPSeeker viewRIP function fails to extract values() in GRangesList/S4 object
RIPSeq
S4
RIP
R
updated 1 day ago by
Ram
43k • written 6.2 years ago by
CrisMar
▴ 80
0
votes
0
replies
1.5k
views
minifi for RRBS
rrbs
batch-effect
methylation
updated 1 day ago by
Ram
43k • written 7.1 years ago by
German.M.Demidov
★ 2.9k
0
votes
0
replies
1.4k
views
Help with Circos plot "Assumption Error" that prevents plotting a protein interactions network
CircosPlot
updated 1 day ago by
Ram
43k • written 3.3 years ago by
hniels01
• 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 5 hours ago by
Ram
43k • written 17 months ago by
Dominique
• 0
1
vote
4
replies
1.3k
views
Splitting long reads into shorter chunks
long-read
updated 13 days ago by
Ram
43k • written 5.8 years ago by
pennakiza
▴ 60
0
votes
0
replies
1.3k
views
which value from ruvadj in missMethyl can present methylation status
R
RUV
methylation
missmethyl
batch-effect
updated 2 days ago by
Ram
43k • written 5.9 years ago by
RC
▴ 20
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect
R
updated 1 day ago by
Ram
43k • written 6.0 years ago by
Jun
• 0
1
vote
2
replies
1.2k
views
Multi-fasta file for gffread
gffread
gtf
fasta
updated 28 days ago by
alnam
▴ 10 • written 2.4 years ago by
Vitor1
▴ 120
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 1 day ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 6.7 years ago by
Dipro
• 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome
PCA
batch-effect
SNP
updated 1 day ago by
Ram
43k • written 4.7 years ago by
Ace
▴ 90
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 1 day ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect
kbet
updated 5 hours ago by
Ram
43k • written 4.0 years ago by
getanid123
• 0
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression
RNA-Seq
updated 9 days ago by
Ram
43k • written 6.4 years ago by
pablo61991
▴ 90
0
votes
0
replies
1.1k
views
Extra adjustment variables during batch effect correction
rna-seq
ComBat
batch-effect
updated 1 day ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 13 days ago by
Ram
43k • written 2.8 years ago by
K
▴ 10
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 3 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
4
replies
1.1k
views
Getting biological replicates from SRA run NCBI
fastq
AWS
SRA
RNAseq
17 days ago by
Andres
▴ 20
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 1 day ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
1
reply
1.1k
views
Ensembl assembly choice for RNA-Seq reference mapping
RNA-Seq
ensembl
STAR
alignment
Assembly
updated 7 days ago by
AHerik
▴ 20 • written 5.0 years ago by
eoin
▴ 30
0
votes
0
replies
1.1k
views
Effect of dbSNP build differences in variant calling
GRCh38
dbSNP
variant-calling
GATK
assembly
updated 23 days ago by
Ram
43k • written 5.4 years ago by
Mehulsharma.253
▴ 30
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 1 day ago by
Ram
43k • written 6.2 years ago by
fawazfebin
▴ 100
0
votes
0
replies
1.1k
views
Isoforms or Duplications
Differential-Gene-Expression
RNA-Seq
updated 9 days ago by
Ram
43k • written 7.1 years ago by
sanathoi
▴ 10
1
vote
0
replies
1.0k
views
interpretation of trajectory and batch effect
monocle3
batch-effect
trajectory
updated 10 days ago by
Ram
43k • written 3.5 years ago by
tushard1987
▴ 10
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 16 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2
RNA-Seq
Differential-gene-Expression
updated 9 days ago by
Ram
43k • written 5.7 years ago by
Pin.Bioinf
▴ 340
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 1 day ago by
Ram
43k • written 4.3 years ago by
akutasame
▴ 40
2
votes
1
reply
947
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression
RNA-Seq
R
DESeq2
updated 9 days ago by
Ram
43k • written 4.0 years ago by
nhaus
▴ 300
2
votes
3
replies
925
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 3 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
1
vote
2
replies
909
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 13 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
7
replies
881
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 23 days ago by
Ram
43k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
881
views
Advice on group specific condition effect and model matrix in deseq2
deseq2
batch-effect
updated 3 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
0
votes
0
replies
865
views
Variant quality scores with different variant caller: HaplotypeCaller vs DeepVariant. How to interpret the quality scores?
variant-calling
DeepVariant
HaplotypeCaller
quality-score
updated 23 days ago by
Ram
43k • written 2.4 years ago by
Jordi
▴ 50
0
votes
2
replies
852
views
freebayes calls presumably homozygous variants as heterozygotes
SNP
freebayes
variant-call
genotyping
updated 13 days ago by
virginia.baraja
• 0 • written 3.1 years ago by
johanna.pieplow
• 0
2
votes
6
replies
847
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 2 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
0
votes
0
replies
832
views
Estimating sequence complexity of DNA sequence from fasta file
sequence
RepeatMasker
pacbio
updated 1 day ago by
Ram
43k • written 5.6 years ago by
epaminonda
▴ 10
0
votes
1
reply
825
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 1 day ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
4
votes
6
replies
824
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 16 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
1
vote
2
replies
819
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 16 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
1
vote
1
reply
809
views
Question for 3 prime bias in rna short read and long read (illumina, ont, pacbio)
rna-seq
short-read
long-read
updated 13 days ago by
Ram
43k • written 11 months ago by
shinyjj
▴ 50
1
vote
2
replies
802
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
525 results • Page
2 of 11
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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