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209 results • Page
1 of 5
Sort: replies
Rank
Views
Votes
Replies
82
votes
46
replies
8.1k
views
15 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 5 days ago by
LauferVA
4.0k • written 9 months ago by
Sasha
▴ 830
70
votes
29
replies
14k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 4 days ago by
jkbonfield
★ 1.2k • written 5.0 years ago by
finswimmer
16k
21
votes
26
replies
9.3k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 4 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
66
votes
23
replies
48k
views
8 follow
extract dendrogram cluster from pheatmap
R
updated 1 day ago by
Getnet Tesfaw
• 0 • written 6.3 years ago by
1769mkc
★ 1.1k
12
votes
19
replies
13k
views
11 follow
SnpMatrix from VCF file
VCF
Eqtl
MatrixEQTL
SnpMatrix
vcftools
updated 4 days ago by
pmiller
▴ 10 • written 7.0 years ago by
Dhana
▴ 110
0
votes
18
replies
854
views
Import list and assign distinct colors in R
R
ggplot2
5 days ago by
kmyers2
▴ 80
105
votes
16
replies
110k
views
16 follow
Convertion Of Gff3 To Gtf
gtf
gff
updated 4 days ago by
xiaoleiusc
▴ 140 • written 11.8 years ago by
GouthamAtla
12k
25
votes
15
replies
7.5k
views
9 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 6 days ago by
Cliff
• 0 • written 12.7 years ago by
2184687-1231-83-
★ 5.1k
8
votes
12
replies
968
views
7 follow
How to speed-up to contruct phylogenetic tree
MEGA
tree
phylogenetic
updated 5 days ago by
Joe
21k • written 3 months ago by
Nelo
▴ 20
3
votes
12
replies
594
views
bbmap read length from fastq
fastq
bbmap
updated 4 days ago by
GenoMax
140k • written 10 days ago by
marco.barr
▴ 30
0
votes
11
replies
617
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 2 days ago by
barslmn
★ 2.1k • written 13 days ago by
avelarbio46
▴ 30
2
votes
10
replies
515
views
Can't properly use GATK Mutect2 to call somatic variants from my tumor/normal samples pair (BAM to VCF)
vaf
gatk
vcf
genomics
mutect2
updated 5 days ago by
GenoMax
140k • written 6 days ago by
Samuel
▴ 20
0
votes
10
replies
734
views
Problem running scPred
scPred
scPredict
updated 5 days ago by
Ram
43k • written 10 weeks ago by
Nitin
• 0
3
votes
10
replies
525
views
Errors running PHG MakeInitialPHGDBPipelinePlugin (**UNASSIGNED**)
pangenome
plants
PHG
updated 4 days ago by
lcj34
▴ 390 • written 6 days ago by
b.contreras.moreira
▴ 10
2
votes
10
replies
662
views
RNA seq aligner?
Alignment
updated 4 days ago by
Dave Carlson
★ 1.6k • written 13 days ago by
tesfaye
• 0
3
votes
10
replies
592
views
t-test in two groups, multiple rows
R
t-test
3 hours ago by
sooni
▴ 20
0
votes
9
replies
453
views
RNA_seq
RNA-seq
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
daffodil
▴ 10
1
vote
9
replies
412
views
miRNA alignment with Bowtie2
bowtie2
3 days ago by
Chironex
▴ 40
14
votes
9
replies
11k
views
8 follow
Downsample BAM file to specific amount of reads
bam
updated 3 days ago by
GenoMax
140k • written 2.6 years ago by
kstangline
▴ 80
1
vote
9
replies
762
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 6 days ago by
Dave Carlson
★ 1.6k • written 7 days ago by
Matthew
• 0
5
votes
8
replies
380
views
Create Conda Environment with YAML File
Python
updated 3 days ago by
dthorbur
★ 1.6k • written 4 days ago by
cthangav
▴ 100
1
vote
8
replies
643
views
6 follow
Using aspera-connect to UPLOAD fastq files to ENA on Linux
ENA
aspera-connect
ascp
updated 3 days ago by
jude
• 0 • written 5 days ago by
sue.jones
• 0
7
votes
8
replies
496
views
Forum:
Bioinformatics career transition
career
forum
updated 4 days ago by
jared.andrews07
★ 16k • written 4 days ago by
jevill17
▴ 20
0
votes
8
replies
1.4k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 4 days ago by
xiangbinruan
• 0 • written 18 months ago by
Phoebe Magdy
• 0
3
votes
8
replies
6.2k
views
6 follow
Download CAZy database
genome
gene
database
cazy
updated 3 days ago by
GenoMax
140k • written 6.1 years ago by
anu014
▴ 190
17
votes
8
replies
4.9k
views
Mean Variance Relationship single cell RNA-Seq Data
RNA-Seq
variance
deseq2
single cell
updated 6 days ago by
thomas.heigl.ibk
• 0 • written 3.2 years ago by
kw486
▴ 30
1
vote
7
replies
323
views
java version compatible with GATK 3.2.2
GATK
6 days ago by
shpak.max
▴ 40
3
votes
7
replies
1.2k
views
7 follow
Transcription Start Site
TSS
updated 31 minutes ago by
Ming Tommy Tang
★ 3.8k • written 23 months ago by
Fatemeh Nabizadeh
▴ 10
0
votes
7
replies
422
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 6 days ago by
Ram
43k • written 6 weeks ago by
Arton
• 0
2
votes
7
replies
498
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 5 days ago by
Chris Dean
▴ 390 • written 6 days ago by
ev97
▴ 20
3
votes
7
replies
3.3k
views
WGCNA adjust p value
statistics
WGCNA
updated 4 days ago by
Ceren
• 0 • written 2.6 years ago by
jason.taotaotan
▴ 10
0
votes
7
replies
1.1k
views
Pan genome of genes
Get_homologues
updated 6 days ago by
b.contreras.moreira
▴ 10 • written 2.9 years ago by
Pedro
• 0
2
votes
7
replies
478
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
6 days ago by
b2003
• 0
0
votes
6
replies
435
views
How to corrected test statistics based on the LDSC intercept?
LDSC
intercept
25 minutes ago by
Isaac
• 0
0
votes
6
replies
550
views
Convert Gene symbol to Ensembl ID
mygene
updated 6 days ago by
Alex Reynolds
35k • written 14 days ago by
r.shiasi3897
▴ 10
4
votes
6
replies
272
views
Protein loops
protein
Loop
4 days ago by
Curious
▴ 10
3
votes
6
replies
485
views
Target deletions with adaptive sampling
microdeletions
nanopore
AdaptiveSampling
6 days ago by
njornet
▴ 10
5
votes
6
replies
398
views
biological meaning /summary for similar sets of GO terms
annotation
GO
updated 6 days ago by
Istvan Albert
100k • written 7 days ago by
lessismore
★ 1.3k
2
votes
6
replies
271
views
Is there anyone who downloaded Azimuth packges?
Azimuth
scRNAseq
updated 4 days ago by
Hatchet
▴ 10 • written 4 days ago by
kayah
• 0
1
vote
5
replies
339
views
UMI_extract for paired end reads of micro_RNA
UMI-tools
UMI
miRNA
updated 6 days ago by
ATpoint
81k • written 7 days ago by
otieno43
▴ 20
1
vote
5
replies
231
views
how to convert SummarizedExperiment files to DESeqDataSet??
scRNA-seq
DEG
DESeq2
updated 6 days ago by
Haci
▴ 520 • written 6 days ago by
kayah
• 0
3
votes
5
replies
341
views
Tutorial for analyzing WGBS data
NGS
methylseq
WGBS
6 days ago by
pt.taklifi
▴ 60
8
votes
5
replies
409
views
Overriding a color palette in R to emphasize specific data points
R
ggplot2
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
jen
▴ 10
3
votes
5
replies
1.6k
views
How to collapse leaves with the same name in ETE3 tree?
python
ete3
updated 3 days ago by
Yogesh
• 0 • written 2.7 years ago by
Andrzej Zielezinski
11k
0
votes
5
replies
366
views
VCF file not being indexed, decided to sort could not sort
bcftools
updated 3 days ago by
LChart
3.8k • written 4 days ago by
hgrsce
• 0
2
votes
5
replies
580
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 4 days ago by
jkbonfield
★ 1.2k • written 5 days ago by
K
• 0
0
votes
5
replies
340
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
5 days ago by
Maxwell
• 0
1
vote
5
replies
1.1k
views
implementation of k-mer counting from krakenuniq to kraken2
metagenomics
kraken2
kraken
krakenuniq
classification
updated 4 days ago by
h.mon
35k • written 12 months ago by
aziznasr1920
▴ 10
2
votes
4
replies
236
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 6 days ago by
Michael
54k • written 6 days ago by
adarsh_pp
▴ 40
0
votes
4
replies
402
views
Simulation of gene level methylation data
simulation
methylation
6 days ago by
Mamatha Y S
• 0
209 results • Page
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Recent Votes
Comment: CAZy database has multiple family sequence...
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential expression at pathway level
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aUser
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Recent Replies
Comment: How to corrected test statistics based on the LDSC intercept?
by
Isaac
• 0
Thank you very much!
Comment: Transcription Start Site
by
Ming Tommy Tang
★ 3.8k
you can use bioconductor as shown in this post using Genomicanges https://support.bioconductor.org/p/46508/
Comment: scRNAseq normalization
by
Ming Tommy Tang
★ 3.8k
To be honest, I really do not use SCT, and use log normalization all the time...
Comment: Subsetting Seurat object based on list of cell barcodes
by
Ming Tommy Tang
★ 3.8k
index<- rownames(seurat.obj_combined) %in% all_good_cells_rhemac10$V1 seurat.obj_combined[index, ] should do the trick
Comment: Average expression of a sample in single-cell data
by
dsull
★ 5.6k
Well, if you're only sequencing the very end (the 3' end) of transcripts, how are you going to detect any of the splice junctions that appe…
Answer: Is it better to pool samples prior to running deseq2, or should the algorithm be
by
swbarnes2
14k
> Seems like pooling all should be statistically more robust. Yup. So put everything into the same DESeq2 object. See: https://…
Answer: Expert Guidance Required for De Novo Transcriptome Analysis
by
Doomhammer
• 0
Do you have enough clean data to assemble, for each genotypes independently? I think at first we should find the difference in transcripts …
Answer: Downloading epigenetic and mutation data of specific TCGA BRCA samples
by
aUser
▴ 30
Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
Thank you so much for your reply! here is what I have after entering the command variableStep#chrom=NT_173277.1 Cavia porcellus strain…
Comment: Differential express genes in imbalance groups
by
Chris
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
by
sooni
▴ 20
It was my mistake. I converted the dataframe to matrix. It works! Thank you!
Comment: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
I do mean the quality of each sample (as measured by residual variability in the linear model, in other words by consistency with other sam…
Comment: Differential express genes in imbalance groups
by
Chris Dean
▴ 390
That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
Answer: Beagle Phasing and Imputation
by
LChart
3.8k
Not doable with older versions of beagle. I seem to recall that it used to be recommended to re-code the sex chromosomes of males in the re…
Answer: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
Imbalanced group sizes are no problem. Just analyse the data as it is. No need to throw data away! For a human study with a large number o…
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