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122,006 results • Page
269 of 2441
Sort: Rank
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0
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0
replies
1.7k
views
Job:
Bioinformatics Research Scientist at CSU
github
HPC
R
python
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
sunetra.das
• 0
0
votes
0
replies
650
views
multiple testing in 450K array data
minfi
methylation
450K
epigenetics
statistics
2.5 years ago by
eebloom
▴ 110
1
vote
0
replies
1.4k
views
Best Practices for CRAM <-> BAM
sambamba
bam
cram
samtools
updated 2.5 years ago by
GenoMax
154k • written 2.5 years ago by
DavidStreid
▴ 110
5
votes
12
replies
3.7k
views
Mean read length from bam file
bam
samtools
updated 2.5 years ago by
seidel
11k • written 2.8 years ago by
shinyjj
▴ 60
1
vote
2
replies
1.6k
views
Using blast to find homologs between two species
blast
orthofinder
homology
updated 2.5 years ago by
Mensur Dlakic
★ 30k • written 2.5 years ago by
Chris
▴ 10
2
votes
3
replies
1.6k
views
batch effect in RNA-Seq
batch-effect
RNA-Seq
updated 15 months ago by
Ram
45k • written 2.5 years ago by
ahmad
• 0
3
votes
6
replies
3.9k
views
Singularity image is not working in nextflow
nextflow
singularity
updated 2.5 years ago by
ATpoint
89k • written 2.5 years ago by
optimistsso4co3
▴ 140
0
votes
4
replies
1.9k
views
Remove string from Seurat object metadata
seurat
scrna
updated 2.5 years ago by
benformatics
4.2k • written 2.5 years ago by
bioinformatics.girl
▴ 30
1
vote
14
replies
3.6k
views
How to calculate the coverage of list of genes in whole exome data
bam
gene
coverage
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
anii
• 0
23
votes
41
replies
8.3k
views
6 follow
I want to correct the erroneous barcode file, and the Python code that I've written, using Biopython, is very slow. How can I make this process fast…
NGS
biopython
illumina
WGS
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
Vijith
▴ 100
0
votes
2
replies
1.2k
views
Trimmomatic(0.33) java error [Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1]
trimmomatic
2.5 years ago by
ebogen
▴ 10
0
votes
1
reply
1.1k
views
How do I integrate GRCh38 CADD v1.6 offline with ANNOVAR?
CADD
v1.6
ANNOVAR
updated 2.5 years ago by
barslmn
★ 2.5k • written 2.5 years ago by
pragnapcu
▴ 10
1
vote
2
replies
1.0k
views
NGS demultiplexing
ngs
demultiplex
2.5 years ago by
SurdanBurasi
• 0
1
vote
1
reply
1.2k
views
News:
20% Off - Bioinformatics Pipeline Development with Nextflow (May 15-17 in Leipzig, Germany)
NGS
nextflow
RNAseq
pipelines
DNAseq
2.5 years ago by
David Langenberger
11k
0
votes
0
replies
575
views
simulated metagenomics datasets
metagenomics
simulated
pbsim3
ONT
dataset
2.5 years ago by
aziznasr1920
▴ 10
0
votes
0
replies
797
views
Unable to create pd file for ChAMP analysis
ChAMP
2.5 years ago by
Monalisa
• 0
0
votes
1
reply
802
views
How to move ColSideColors to the bottom of the heatmap using heatmap.2?
heatmap.2
gplots
2.5 years ago by
kopelol
▴ 20
0
votes
1
reply
780
views
Line chart plotting
plot
rtPCR
PCR
Linux
shell
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
Adyasha
• 0
2
votes
2
replies
1.3k
views
running Juicer "awk: syntax error"
awk
2.5 years ago by
Jarjayes
▴ 10
0
votes
3
replies
2.5k
views
Issue in installing any package in R
BiocManager
seurat
R
updated 2.5 years ago by
jv
★ 1.9k • written 2.5 years ago by
sidrah.maryam
▴ 70
0
votes
1
reply
823
views
pipeline for correlation of RNASeq and Methylation data
rnaseq
methylation
correlation
normalization
data
updated 2.5 years ago by
Papyrus
★ 3.1k • written 2.5 years ago by
Omics data mining
▴ 260
4
votes
5
replies
3.2k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 18 months ago by
Ram
45k • written 2.5 years ago by
luffy
▴ 130
3
votes
6
replies
3.2k
views
when to use trimmomatic
trimmomatic
multiqc
sra
updated 2.5 years ago by
Meisam
▴ 250 • written 2.5 years ago by
Nelo
▴ 20
5
votes
6
replies
8.0k
views
R scripting - cannot coerce type 'closure' to vector of type 'character'
Linux
ggplot
R
updated 2.5 years ago by
zx8754
12k • written 2.5 years ago by
Adyasha
• 0
3
votes
2
replies
888
views
Writing lengths of fasta sequences to another file
sequencing
Python
Fasta
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
Hau
▴ 10
2
votes
5
replies
3.8k
views
6 follow
How can I make all my PCA plots the same shape using ggplots?
deseq2
axis
ggplots
updated 2.5 years ago by
noodlejackson
▴ 40 • written 2.5 years ago by
mgranada3
▴ 60
0
votes
2
replies
1.1k
views
Is it possible to use limma to simultaneously analyze RNA-seq and gene expression array data?
limma
RNA-seq
Affy
updated 2.5 years ago by
Gordon Smyth
★ 8.3k • written 2.5 years ago by
njbernstein
▴ 40
0
votes
5
replies
2.1k
views
Update MitoZ 3.4 to 3.5
ubuntu
mitoZ
updated 2.5 years ago by
linzhi2013
• 0 • written 2.5 years ago by
manaswiniparija3
▴ 60
1
vote
1
reply
2.4k
views
How to use the clustal omega command line tool with custom gap penalty?
clustal-omega
multiple-sequence-alignment
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
sodiumnitrate
▴ 20
2
votes
3
replies
1.1k
views
NCBI Relevant files not being returned as query results. Trying to build exhaustive dataset.
NCBI
Entrez
BioPython
updated 2.5 years ago by
GenoMax
154k • written 2.5 years ago by
chordata
• 0
0
votes
2
replies
1.1k
views
Do I need to specify the introns on the gtf file for cellranger?
fasta
gtf
cellranger
scRNAseq
updated 2.5 years ago by
GenoMax
154k • written 2.5 years ago by
bioinfo
▴ 160
5
votes
2
replies
1.3k
views
Spearman correlation rna-seq gene to blood values
spearman
rna-seq
updated 2.5 years ago by
ATpoint
89k • written 2.6 years ago by
bas2020
▴ 60
1
vote
5
replies
1.5k
views
Number of allelic depths is larger than number of inferred alleles in VCF file
VCF
GATK
Genotyping
Variant-calling
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
Alexandros
• 0
1
vote
2
replies
1.1k
views
Do Benjamini-Hochberg p.adj values get less strict when analysing only one superfamily only? RNA-seq
pvalue
p-value
rna-seq
Benjamini-Hochberg
updated 2.5 years ago by
Istvan Albert
103k • written 2.5 years ago by
noodlejackson
▴ 40
11
votes
3
replies
1.6k
views
Whole genome comparison of two closely related plant species
mummer
comparative-genomics
whole-genome-alignment
whole-genome-comparison
mauve
updated 2.5 years ago by
SanjidaR_NCBI
▴ 70 • written 2.5 years ago by
LDT
▴ 340
0
votes
2
replies
1.1k
views
error_in _running_RepeatModeler
ubuntu
RepeatModeler
updated 2.5 years ago by
GenoMax
154k • written 2.5 years ago by
manaswiniparija3
▴ 60
4
votes
2
replies
1.1k
views
R programming scripting linux bioinformatics
Linux
shell-scripting
R
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
Confused_human
▴ 30
5
votes
7
replies
4.8k
views
Download many NCBI genomes with list of GCA identifiers
genomes
biopython
ncbi
api
python
updated 2.5 years ago by
Mensur Dlakic
★ 30k • written 2.5 years ago by
0fbcb0a9
• 0
0
votes
1
reply
797
views
Pair files
methylation
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
Shaimaa Gamal
▴ 10
0
votes
3
replies
1.6k
views
htseq-count : dosen't show options in bash ln ubuntu
linux
Htseq-count
updated 2.5 years ago by
WouterDeCoster
48k • written 2.5 years ago by
Foad
▴ 10
5
votes
4
replies
1.9k
views
No Replicate RNA-Seq (But still biological replicates)
replicates
RNA-Seq
2.5 years ago by
noodlejackson
▴ 40
0
votes
0
replies
517
views
Making a classifier across array types
microarray
random
forest
normalization
yugene
R
2.5 years ago by
Llander
• 0
0
votes
0
replies
1.6k
views
Job:
Looking for internship in boinformatics
plant-genetics
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
iqrajaved323
• 0
1
vote
6
replies
3.9k
views
Error in MuscleCommandline (biopython)
Biopython
Multiple-Sequence-Alignment
Python
updated 2.5 years ago by
Philipp Bayer
8.9k • written 3.2 years ago by
Plus
▴ 20
1
vote
1
reply
810
views
How can I make a similar mutated gene expression figure with TCGA data
cancer
RNA-Seq
FireBrowse
TCGA
updated 2.5 years ago by
tomas4482
▴ 430 • written 2.5 years ago by
valgenome
• 0
1
vote
2
replies
2.8k
views
How to rerun Guppy Basecalling (with both fast5_pass and fast5_fail)
guppy
Nanopore
2.5 years ago by
Ludwig Kian Soon
• 0
0
votes
2
replies
1.3k
views
Forum:
How to start in bioinformatics?
career
updated 2.4 years ago by
Ram
45k • written 2.5 years ago by
caffrey
• 0
0
votes
0
replies
622
views
How to isolate mitochondrial RNA and perform an RNA-seq analysis from cultured cell?
proteome
RNA
isolate
RNA-seq
mitochondrial
2.5 years ago by
diego1530
▴ 80
1
vote
2
replies
1.1k
views
Seeking feedback on RNA-seq analysis with low sample size and custom pathways
RNA
sequencing
DESeq2
updated 2.5 years ago by
noodlejackson
▴ 40 • written 2.5 years ago by
Anne
• 0
0
votes
1
reply
757
views
Congena (Co-expressed gene-set enrichment analysis) Input?
gen
ontology
COGENA
pathway
updated 2.5 years ago by
rpolicastro
13k • written 2.5 years ago by
omargmc.tak
• 0
122,006 results • Page
269 of 2441
Recent Votes
Comment: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
Answer: GUI commercial software for 10x single cell gene expression analysis
GUI commercial software for 10x single cell gene expression analysis
Answer: FACS quality control based on size and doublet detection in scRNA-seq
Answer: FACS quality control based on size and doublet detection in scRNA-seq
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Comment: GUI commercial software for 10x single cell gene expression analysis
by
Istvan Albert
103k
A comment on: "*Wonky analysis is possible even with open-source R libraries.*" True - and arguably, the risk of a wonky analysis is actua…
Comment: GUI commercial software for 10x single cell gene expression analysis
by
GenoMax
154k
`Trailmaker` likely only supports Parse's evercode data. <br> `BioTuring` does not appear to have published pricing. <br> `Rosalind` appear…
Answer: GUI commercial software for 10x single cell gene expression analysis
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Found a few more when I asked around. I have no idea how good or bad these are. If anyone has used these or knows more about these, feel fr…
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> I performed a standard proteomics screening workflow What database did you use to search against? Perhaps you are using an old (not so c…
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No, it's unrelated. Doublets in 10x happen if two cells get enclosed into the same GEM droplet. This has nothing to do with how flow cytome…
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Apparently you are working with human proteins? I would strongly recommend looking only at proteins that are part of the human reference pr…
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8.0k
Wow, thats too long. How much RAM does your machine have, it is likely swapping
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★ 2.4k
Note that UniProtKB accession numbers do not have any meaning. While most ACs starting with A0A5* are indeed unreviewed (i.e. from TrEMBL),…
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▴ 240
Thank you but sorry, your answer sounds very AI-based...
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For basic analysis, discard anything that isn't from Swiss-Prot. Your statistics and pathway analysis should only be based on reliable, ann…
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▴ 160
For a 200-SNP panel at your sample throughput, I would recommend an amplicon-based targeted sequencing approach. The workflow involves des…
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dthorbur
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There are *a lot* of factors that can impact the number of identified SNPs. These include things like: - Evolutionary distance from samp…
Answer: DESeq2 on metagenome KO counts
by
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▴ 160
Your proposed workflow is indeed sound, as applying DESeq2 to KO-counts is perfectly valid; its underlying negative binomial model is metho…
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The massive difference has been reproducible across the 3 biological replicates and is in line with what we would expect in terms of the bi…
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My initial concern is the ~15-fold difference (450 vs 7500) between called peaks in the two different cell line conditions. This suggests t…
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