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156 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
1
vote
0
replies
106
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
5 days ago by
fr
▴ 200
1
vote
2
replies
216
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 3 days ago by
thadjudkins2
• 0 • written 4 days ago by
herh
• 0
1
vote
3
replies
208
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 4 days ago by
GenoMax
129k • written 5 days ago by
NikhilP
▴ 20
1
vote
3
replies
702
views
Regular Expression for conversion
Linux
grep
updated 6 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
2
replies
226
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
13 hours ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
90
views
How to perform a phylogenetic analysis from a vcf file
variants
haplotyping
phylogeny
vcf
1 day ago by
rj.rezwan
• 0
0
votes
0
replies
178
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
6 days ago by
Vincent Laufer
★ 2.9k
0
votes
0
replies
69
views
Prediction of altrered metabolites from altered gene expression
Gene
Metabolites
1 day ago by
english.server
▴ 290
0
votes
0
replies
104
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
5 days ago by
mbk0asis
▴ 660
0
votes
0
replies
535
views
Online courses/studies bioinformatics
online-study
learning
updated 3 days ago by
Ram
39k • written 3.8 years ago by
MAR
• 0
0
votes
1
reply
754
views
Where can I find Time Series Multi-Omics human cancer datasets
multi-omics
cancer
time-series
updated 6 days ago by
Ram
39k • written 3.2 years ago by
donnieDarko
• 0
0
votes
4
replies
273
views
Identification of genes involved in my pathway
KEGG
keggGet
4 days ago by
smanzano250800
• 0
0
votes
0
replies
111
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
5 days ago by
Maddie
• 0
0
votes
4
replies
349
views
What are recommended parameters for the local protein alignment ?
protein
alignment
2 days ago by
Alexander
▴ 70
0
votes
0
replies
119
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
3 days ago by
Omics data mining
▴ 220
0
votes
0
replies
74
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 17 hours ago by
Ram
39k • written 18 hours ago by
B.N.
• 0
0
votes
0
replies
165
views
Chipseq data peak calling issue
ChIP-seq
RNA
sequencing
updated 6 days ago by
Ram
39k • written 11 days ago by
Adyasha
• 0
0
votes
3
replies
219
views
hardfilter error
bam
recall
3 days ago by
bestone
▴ 10
0
votes
0
replies
75
views
1000G reference panel for LD clumping
LD
6 days ago by
en_keser
• 0
0
votes
0
replies
605
views
Pan-genome Bioinformatics Workshops?
pan-genome
workshop
updated 16 hours ago by
Ram
39k • written 3.7 years ago by
cassondranewman
• 0
0
votes
0
replies
144
views
jellyfish options
kmer
jellyfish
3 days ago by
Tele
• 0
0
votes
0
replies
61
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 18 hours ago by
Ram
39k • written 20 hours ago by
beausoleilmo
▴ 530
0
votes
0
replies
1.7k
views
Artificial Neural Networks applied to environmental data
artificial-neural-networks
time-series
ANN
updated 6 days ago by
Ram
39k • written 8.6 years ago by
felipehcoutinho
▴ 10
0
votes
0
replies
866
views
Error processing Hi-data using HiCUP
NGS
HiCUP
Hi-C
updated 5 days ago by
Ram
39k • written 4.0 years ago by
srhic
▴ 40
0
votes
0
replies
131
views
Per base sequence content warning in ChIPseq data FastQC analysis
ChIP-seq
FastQC
updated 6 days ago by
Ram
39k • written 5 weeks ago by
shashianand15
• 0
0
votes
3
replies
307
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
1 day ago by
eimanpharmacist
▴ 20
0
votes
0
replies
129
views
Differential protein expression analysis
R
proteomic
statistics
2 days ago by
Ribo
▴ 40
0
votes
0
replies
97
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
5 days ago by
Apprentice
▴ 140
0
votes
1
reply
159
views
Merge different vcf files
vcf
updated 3 days ago by
Ram
39k • written 4 days ago by
caique.manochio
• 0
0
votes
1
reply
749
views
plasmid spades R1/R2 files?
plasmid
sequencing
updated 3 days ago by
Ram
39k • written 3.7 years ago by
sarah.goldstein
• 0
0
votes
0
replies
84
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
6 days ago by
saladi
▴ 30
0
votes
0
replies
194
views
Bed files of narrowPeak in ENCODE
ENCODE
updated 6 days ago by
Ram
39k • written 4 weeks ago by
younglin113
▴ 50
0
votes
1
reply
155
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 6 days ago by
GenoMax
129k • written 6 days ago by
fafad046
• 0
0
votes
0
replies
460
views
Error running gene expression based ProTINA
ProTINA
Time-Series
gene-expression
updated 6 days ago by
Ram
39k • written 2.5 years ago by
Omics data mining
▴ 220
0
votes
0
replies
138
views
IGV insertions
insertions
IGV
3 days ago by
christoph.schubart
• 0
0
votes
0
replies
1.3k
views
Cuffdiff with 2 conditions and time series
cuffdiff
time-series
RNA-Seq
transcriptome
updated 6 days ago by
Ram
39k • written 6.2 years ago by
KL
• 0
0
votes
0
replies
643
views
What option should I use for show me result which I can filter my data by their p-value and FC?
MASIGPRO
Time-Course
RNA-Seq
updated 6 days ago by
Ram
39k • written 3.4 years ago by
sabaghianamir70
▴ 70
0
votes
1
reply
813
views
Filtering for homozygous reference alleles
SNP
sequence
genome
updated 3 days ago by
Ram
39k • written 3.7 years ago by
AGE
▴ 30
0
votes
0
replies
11
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
2 hours ago by
hashim.rana11
▴ 20
0
votes
4
replies
790
views
Detecting Biomarkers from Time Series Gene Epression data
Time-Series
Gene-Expression
Biomarkers
updated 6 days ago by
Ram
39k • written 3.2 years ago by
donnieDarko
• 0
0
votes
1
reply
684
views
Small demo bioinformatics workflows which don't require reference data?
workflow
pipeline
updated 3 days ago by
Ram
39k • written 3.7 years ago by
steve
★ 3.3k
0
votes
0
replies
1.1k
views
EDGE microarray time series analysis fit_models() ERROR
microarray
time-series
updated 6 days ago by
Ram
39k • written 5.4 years ago by
tleona3
▴ 10
0
votes
0
replies
455
views
Normalizing multiple conditons all together
RMA
microarray
time-series
updated 6 days ago by
Ram
39k • written 2.6 years ago by
Raheleh
▴ 250
0
votes
1
reply
873
views
Masters in Bioinformatics
masters
structural-bioinformatics
assistantship
updated 4 days ago by
Ram
39k • written 3.9 years ago by
Manvitha Reddy
▴ 10
0
votes
3
replies
204
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 5 days ago by
andres.firrincieli
3.4k • written 6 days ago by
kamanovae
▴ 80
0
votes
1
reply
137
views
Pairwise Alignment
Pairwise-Alignment
updated 18 hours ago by
Ram
39k • written 1 day ago by
Fatemeh
• 0
0
votes
3
replies
192
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
4 days ago by
Mohd
▴ 20
0
votes
0
replies
131
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
2 days ago by
Manuel
• 0
0
votes
2
replies
611
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 6 days ago by
Ram
39k • written 13 months ago by
Meeran
• 0
0
votes
0
replies
105
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 5 days ago by
Ram
39k • written 5 days ago by
Mah
• 0
156 results • Page
2 of 4
Recent Votes
Visualizing Graph Alignment Format via minigraph
Gene prediction software
ClusterProfiler : What is GeneRatio and BgRatio?
ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
A: ClusterProfiler : What is GeneRatio and BgRatio?
Get relationships and hierarchies for GO terms
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Recent Replies
Answer: Visualizing Graph Alignment Format via minigraph
by
colindaven
4.8k
That's a really good question. Short version: not much to my knowledge, aside from looking at it, or filtering it (as it's a PAF like forma…
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
BTW - Most TCGA cancer types do have normals amoungst the samples.
Comment: Alignment of case vs. control from different origin
by
i.sudbery
17k
The assumption of these studies is that any batch effect within a batch affects both treatment and control equally, so that when you divide…
Answer: Stratified sample assignment for analysis
by
Vincent Laufer
★ 2.9k
First, you didn't tell us what kind of data you are working with. For arguments sake, I'll assume bulk RNA-seq. Generally, your options …
Comment: VEP tab/vcf - Different output
by
Ben_Ensembl
★ 2.2k
You can use the ---show_ref_allele flag when running the VEP query. This will add the reference allele in the output and is mainly useful f…
Comment: Get relationships and hierarchies for GO terms
by
Alexander
▴ 70
For R-users might be interesting to look at notebook "CAFA5: train set GO terms" https://www.kaggle.com/code/antoninadolgorukova/cafa5-trai…
Comment: Getting Pairwise Sequence Alignment Score With Biopython
by
Alexander
▴ 70
Thanks for sharing ! Just these days I am trying to wrap my mind on protein alignments. I wonder: 1) "PID" in your post is "percentage o…
Answer: What kind of statistical test does Cellranger count use?
by
fracarb8
▴ 950
You should read the [cellranger documentation][1] to understand how the analysis are performed. For example, it uses `graphclust` for clust…
Answer: Gene prediction software
by
alexandru.bologa.marian
▴ 40
Hi, I don't know if there are tools designed to predict pseudogenes, but If i understand correctly from your post you could predict all th…
Answer: Getting Pairwise Sequence Alignment Score With Biopython
by
Jonathan Lefebre
▴ 60
Maybe quite late, but in case other people are looking for this. Pairwise sequence identity can be easily calculated using basic python fun…
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
Yes, that is what methylkit is for. See my answer.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.
Comment: Installation of PPFinder
by
subashini.fbtpb106
▴ 10
Can you suggest me any software that does gene prediction by masking pseudogenes?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
IMHO this is like asking for the cow when you only have a steak :-)
Comment: Getting same value for start and end position, "DNA methylation"
by
Pankaj
• 0
yes I am working on Bisulphate sequenced data.
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