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78 results • Page
1 of 2
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10
votes
6
replies
2.6k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 19 hours ago by
Ram
38k • written 7.8 years ago by
lait
▴ 170
3
votes
2
replies
141
views
Power analysis for patient samples
RNA-seq
21 hours ago by
aropri
▴ 130
3
votes
4
replies
221
views
Creating sample groups from a combination of genes for survival analysis
Survival
6 hours ago by
krushnach80
★ 1.1k
3
votes
3
replies
334
views
Retrieving information from FASTA file
NGS
FASTA
VCF
updated 19 hours ago by
Ram
38k • written 12 months ago by
Maryam
▴ 10
3
votes
2
replies
204
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
PAAD
KM
Plot
TCGA
26 minutes ago by
Manav
• 0
2
votes
3
replies
506
views
BWA generating a sam file without alignment information
sam
bwa
updated 18 hours ago by
Ram
38k • written 13 months ago by
kelsey.e.witt
• 0
2
votes
7
replies
766
views
Import data for igraph using R
r
igraph
updated 19 hours ago by
Ram
38k • written 12 months ago by
kaisakaiho73847
• 0
2
votes
6
replies
1.0k
views
GFF3 TO GTF CONVERSION
GFF3
Hydra
GFF
GTF
updated 18 hours ago by
Ram
38k • written 14 months ago by
Shagnik
• 0
2
votes
5
replies
90
views
getting coding exon information from Ensembl API
API
Esembl
15 minutes ago by
Sarah
▴ 30
2
votes
5
replies
526
views
msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 19 hours ago by
igor
13k • written 4 days ago by
e.r.zakiev
▴ 30
1
vote
1
reply
3.3k
views
How do I find cross-reactive species given two primers?
primer
blast
updated 18 hours ago by
Ram
38k • written 7.8 years ago by
andytsaica
• 0
1
vote
6
replies
1.0k
views
gff file
GFF
UNIPRTOT
updated 58 minutes ago by
Ram
38k • written 18 months ago by
devhimd
▴ 10
1
vote
2
replies
455
views
CONECT part in the pdb file
python
pandas
pdb
updated 19 hours ago by
Ram
38k • written 11 months ago by
Elsaid
• 0
1
vote
5
replies
284
views
Plot heatmap using row_splitting but splitting should based on a column in dataset - ComplexHeatmap
R
row_split
ComplexHeatmap
updated 21 hours ago by
Trivas
▴ 680 • written 1 day ago by
TJay
• 0
1
vote
4
replies
346
views
Loading Traitdata file for WGCNA analysis
R
WGCNA
updated 23 hours ago by
Ram
38k • written 5 months ago by
priya.bmg
▴ 50
1
vote
1
reply
455
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 19 hours ago by
Ram
38k • written 10 months ago by
ManuelDB
▴ 30
1
vote
8
replies
1.2k
views
Loading a pre-filtered loom file into pySCENIC
scRNA-seq
pySCENIC
loom
updated 20 hours ago by
Ram
38k • written 7 months ago by
Jacob
• 0
1
vote
3
replies
101
views
Is it ok to trim assembled paired-end fastq files with cutadapt 3.4 ?
QC
cutadapt
Illumina
trimming
3.4
updated 2 hours ago by
GenoMax
127k • written 5 hours ago by
Bengisu
• 0
1
vote
2
replies
94
views
What is exactly meant by "GENCODE TSS"?
GENCODE
transcription
annotation
TSS
gene
updated 3 hours ago by
ntsopoul
▴ 50 • written 5 hours ago by
ConvolutedGenome
▴ 10
1
vote
1
reply
66
views
RNAseq: same reads + more complete scaffold = fewer DEGs?
RNAseq
updated 3 hours ago by
Darked89
4.2k • written 4 hours ago by
phillip.brassington
▴ 10
1
vote
1
reply
111
views
NA14622 data for benchmarking
benchmarking
vcf
bed
GiAB
updated 23 hours ago by
GenoMax
127k • written 1 day ago by
emmanouil.a
▴ 110
1
vote
2
replies
45
views
Geom bar postive and negative values in a flipped plot
flip_coord
ggplot
geom_bar
updated 1 hour ago by
bas2020
• 0 • written 3 hours ago by
luzglongoria
▴ 40
1
vote
1
reply
379
views
LFTP fails to submit files to the EGA sequence database
lftp
EGA
updated 19 hours ago by
Ram
38k • written 10 months ago by
heskett
▴ 100
1
vote
2
replies
417
views
Read multi-fasta into Python and search by nucelotide
fasta
python
updated 18 hours ago by
Ram
38k • written 15 months ago by
prityreem1
• 0
0
votes
2
replies
167
views
mrbayes segmentation fault
mrbayes
segmentation
fault
1 hour ago by
dgrace999
• 0
0
votes
0
replies
456
views
How to plot heatmap for the matrix for the pairwise comparison of sequence similarity in python?
heatmap
python
distance-matrix
updated 18 hours ago by
Ram
38k • written 15 months ago by
ramsha
• 0
0
votes
2
replies
113
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
10 minutes ago by
Sian
• 0
0
votes
2
replies
1.3k
views
Intersection of flow cytometry and bioinformatics
flow-cytometry
updated 23 hours ago by
Ram
38k • written 6.3 years ago by
singh.bioinfo
▴ 30
0
votes
0
replies
76
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
14 hours ago by
rheab1230
▴ 140
0
votes
7
replies
1.1k
views
Unable to convert from sam to bam file.
bam
sam
samtools
updated 18 hours ago by
Ram
38k • written 14 months ago by
usef
• 0
0
votes
0
replies
229
views
Tapestry scDNA-seq and translocations
scDNA-seq
H5
single-cell
MOSAIC
variant-calling
updated 19 hours ago by
Ram
38k • written 11 months ago by
jmnz22
• 0
0
votes
0
replies
165
views
MEME motif discovery
fasta
updated 19 hours ago by
Ram
38k • written 10 months ago by
kaisakaiho73847
• 0
0
votes
0
replies
426
views
Measure genome-wide agreement of peaks in
bigwig
atac-seq
macs2
updated 23 hours ago by
Ram
38k • written 17 months ago by
Al Murphy
▴ 30
0
votes
2
replies
134
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
4 hours ago by
HERMAN
▴ 10
0
votes
0
replies
28
views
Outgroup for plastome NJ-tree (from pseudoalignment based on SNPs)
bwa-mem2
samtools
freebayes
mega
vcf2phylip
2 hours ago by
poecile.pal
▴ 50
0
votes
0
replies
189
views
Comparing PopoolationTE2 output with reference .bed file in Python
bed
python
pandas
PopoolationTE2
updated 20 hours ago by
Ram
38k • written 8 months ago by
Emilia
• 0
0
votes
0
replies
49
views
Hi-C aggregation plot | ARA | PE-Scan
Hi-C
5 hours ago by
Argonaut
• 0
0
votes
2
replies
330
views
Can't create index file of Bam file
bam
samtools
updated 20 hours ago by
Ram
38k • written 7 months ago by
Zahed Alam
• 0
0
votes
3
replies
399
views
splitting a bam file by XA tag into multiple lines
bam
BWA
updated 20 hours ago by
Ram
38k • written 9 months ago by
eric.londin
▴ 50
0
votes
0
replies
277
views
SURVIVOR bed file
BED
CNV
SURVIVOR
VCF
updated 20 hours ago by
Ram
38k • written 8 months ago by
Nameless
• 0
0
votes
0
replies
382
views
Using infercnv R package
r
infercnv
Seurat
annotation
updated 23 hours ago by
Ram
38k • written 6 months ago by
j.jacob1
• 0
0
votes
1
reply
282
views
Batch rename fasta file of RefSeq
fasta
refseq
updated 20 hours ago by
Ram
38k • written 7 months ago by
BATMAN
• 0
0
votes
3
replies
427
views
GC @5,20,50 : Fraction of GC content in the bases around the variant position
fasta
genome
GC-content
updated 19 hours ago by
Ram
38k • written 10 months ago by
Maryem
▴ 10
0
votes
0
replies
54
views
displaying results of different RNA-seq projects in R shiny
RNA-seq
shiny
R
4 hours ago by
rls_08
▴ 40
0
votes
2
replies
401
views
How to remove evidence tags and unnecessary information in the uniprot tab file
UNIPROT
updated 19 hours ago by
Ram
38k • written 10 months ago by
devhimd
▴ 10
0
votes
0
replies
158
views
How to generate a bed file indicating increased ratio of H3K4me3 to H3K4me1
H3K4me3
bed
H3K4me1
updated 19 hours ago by
Ram
38k • written 10 months ago by
jia
• 0
0
votes
0
replies
44
views
calc IBS with vcf files
IBS
PLINK
4 hours ago by
Mali
• 0
0
votes
2
replies
349
views
how to calcul risk score with a prognostic genes
riskscore
multivariate
analysis
prognostic
model
3 hours ago by
Sarah
▴ 30
0
votes
0
replies
338
views
Validation of Bioinformatics pipeline with NA12763
hap.py
updated 23 hours ago by
Ram
38k • written 23 months ago by
esimonova.me
▴ 20
0
votes
0
replies
189
views
How to convert .bed/.bim/.fam file to .dat file to run --dosage command to get INFO
plink
dosage
updated 20 hours ago by
Ram
38k • written 9 months ago by
Raju
• 0
78 results • Page
1 of 2
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A: Using GATK's HaplotypeCaller or Mutect2 for somatic cancer samples with no norma
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
Comment: Where do find virulence gene information in a gff/gtf file?
Comment: Where do find virulence gene information in a gff/gtf file?
Comment: Where do find virulence gene information in a gff/gtf file?
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Recent Replies
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
Sian
• 0
Unfortunately yes, there does seem to be a problem with using the older version - when I came to do more analysis yesterday, the enrichKEGG…
Comment: getting coding exon information from Ensembl API
by
Sarah
▴ 30
Because you just answer when it's a stupid question or when I ask a lot of questions. This is for asking questions not for being judged by …
Comment: KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
by
Manav
• 0
Thanks, tried working with the dataset and workflow. It worked.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
BioinfoBee
• 0
@juke34 Thanks again. I changed the config.yaml *should overlapping loci (at CDS level) be merged in a single locus Only one gene is kept,…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
Thanks, I am not doing any differential. But, Can we say that 6th transcript is relatively more abundance in our sample than other transcri…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
zrm22
▴ 30
It looks like the ImputePipelinePlugin for the minimap2 run does not use the numThreads Option but rather does the numThreadsOnMachine - 2 …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
@rob Please, Can you or people from your group answer . As I am using one of your paper as my [reference.][1] [1]: https://f1000rese…
Comment: fastq_screen error: Failed to calculate read length
by
firestar
★ 1.5k
I created the .fasta from a BAM, so I am just going to go back to the BAM and convert that to a .fastq and see if that works. But good to k…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
Ram
38k
> I have only one condition There is no "differential" then. RNAseq is a relative measure, so comparing single-condition replicates using …
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
[Salmon][1] is giving me TPM at transcript level. So, What I understand from that TPM is normalized for sequencing depth and Transcript l…
Answer: Does it possible to know what are the adjacent genes up to 1000bp upstream and
by
Alex Reynolds
34k
You could use `bedmap` from BEDOPS. Say you have a BED file of IS/transposable elements called `elements.bed` and a BED file of genes calle…
Comment: Java -xmx option does not limit memory usage in the ImputePipelinePlugin?
by
twrl8
• 0
Ahh thank you! I thought the xmx parameter would be passed to the downstream commands called by the plugin. Then I think I definitely need…
Comment: mrbayes segmentation fault
by
dgrace999
• 0
Hello, Thank you. An explanation of where I came up with 2500 is 10 million divided by 1000 (because sample freq is 1000), divided again b…
Answer: How to extract proteins from PCs in plot_pca in DEP package?
by
ATpoint
70k
You can run PCA yourself with only few lines of code. See here under PCA https://www.biostars.org/p/461026/ You can then use the prcomp ou…
Comment: Can I use abundance from Tximport to compare the expression level of transcript
by
aimanbarki
▴ 20
DESeq2 is for Differential gene analysis. I also tried DEXSeq (DEU) and DRIMSeq [DTU][1]) but my issue is the following: 1. I have only one…
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